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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Too few genes with valid expression levels in the required number of samples. #244

Closed yamihn closed 1 month ago

yamihn commented 1 month ago

Hi, I imputed my dataset using MAGIC and I would use the imputed data in a cluster to find modules. reached getOption("max.print") -- omitted 3 rows ]

> head(assay_data, 3)
        KO1b__AAGCGTTGTGGTACAG-1 KO1b__AGCCAATGTAGGACTG-1 KO1b__AGCTCAATCTTCGCTG-1 KO1b__AGGATCTGTAGCGTCC-1 KO1b__AGGTCTACATTCCTCG-1
Xkr4                 0.177204122              0.151632245              0.067603215              0.190768090              0.059037204
Gm1992               0.003720510              0.007810524              0.001524137              0.003868197              0.006116687
Gm19938              0.005767166              0.012638044              0.082680874              0.003613595              0.087701380
        KO1b__AGTGCCGGTCTTCGAA-1 KO1b__ATGAGGGTCAGAATAG-1 KO1b__ATTTCTGGTTCCAGGC-1 KO1b__CAACCAAAGCCGAATG-1 KO1b__CAGATCAAGCCTCAAT-1
Xkr4                 0.194352165              0.191548144              0.174918546              0.059873856              0.154019471
Gm1992               0.002876425              0.002639006              0.003921483              0.002908296              0.003595854
Gm19938              0.003695571              0.003160934              0.006671532              0.083990257              0.017696571
        KO1b__CCGATCTTCGTGCATA-1 KO1b__CCGGTAGGTTGCTTGA-1 KO1b__CCGTAGGGTCCATACA-1 KO1b__CGAGAAGCACGGCTAC-1 KO1b__CGGACACGTCACAGTT-1
Xkr4                 0.069849906              0.122907001              0.183481431              0.098911095              0.166761790
Gm1992               0.003255042              0.009425501              0.004960533              0.001235264              0.003911654
Gm19938              0.075164336              0.006409602              0.006458909              0.062929863              0.011665866
        KO1b__CGGGACTAGCGTCAAG-1 KO1b__CGTTGGGTCGAGTGGA-1 KO1b__CTCAGGGAGCGCCTCA-1 KO1b__GAATCGTTCATCTCTA-1 KO1b__GACACGCTCTCCACTG-1
Xkr4                  0.19068486              0.077006427              0.192035231              0.079681175              0.147470855
Gm1992                0.00350144              0.001819175              0.001925022              0.004509914              0.009992537
Gm19938               0.00350927              0.074210663              0.004070490              0.074095806              0.017918294
        KO1b__GATCACAGTGGGTATG-1 KO1b__GATTCGAGTGAACTAA-1 KO1b__GATTGGTTCGGTCTGG-1 KO1b__GCTGCAGAGCGTGAAC-1 KO1b__GGAATCTCATCCCGTT-1
Xkr4                 0.068685049              0.080789318              0.194148940              0.256748506              0.157601535
Gm1992               0.003457021              0.002392877              0.002198848              0.018894762              0.005587798
Gm19938              0.082692169              0.076069684              0.003217430              0.002068376              0.011253916
        KO1b__GGGTTTAGTATGCAAA-1 KO1b__GGTGTCGGTGGGCTCT-1 KO1b__GTAGCTACAAATGGTA-1 KO1b__GTCAAGTTCCGAACGC-1 KO1b__GTGAGCCTCGGCTGTG-1
Xkr4                 0.170577800               0.12576769              0.199994011              0.182042455               0.07588650
Gm1992               0.001371684               0.00585926              0.001347588              0.001881719               0.00473530
Gm19938              0.026979674               0.02954680              0.002618236              0.004521843               0.07684179
        KO1b__GTGGAAGCAGCAGTAG-1 KO1b__GTGGAAGGTCTTACAG-1 KO1b__GTTATGGAGCTGACCC-1 KO1b__GTTCCGTAGCGGCTCT-1 KO1b__TAAGCGTTCCGTAGTA-1
Xkr4                  0.14517650              0.178381454              0.180894579               0.18032249              0.158581527
Gm1992                0.02244986              0.003820932              0.002049146               0.01823765              0.004355174
Gm19938               0.04249093              0.006724114              0.004367883               0.02041376              0.016828411
        KO1b__TATTCCATCTTTCCAA-1 KO1b__TATTGGGCATTGAAAG-1 KO1b__TCATCCGAGGATCACG-1 KO1b__TCATCCGTCTCCGCAT-1 KO1b__TCCGAAATCGTGGAAG-1
Xkr4                 0.058591340              0.181716205              0.199561369               0.15539052              0.183987282
Gm1992               0.005893258              0.004455526              0.002731332               0.00370774              0.003494017
Gm19938              0.090703701              0.005885544              0.002681780               0.02517122              0.008762390
        KO1b__TCCTCTTCATCCGAAT-1 KO1b__TCCTTTCTCTACTTCA-1 KO1b__TGACCCTTCACCTCGT-1 KO1b__TGTCCCATCGGTTGTA-1 KO1b__TTACCATTCCCAGTGG-1
Xkr4                 0.171951930              0.057612023               0.05673751              0.175421197              0.081449712
Gm1992               0.006693962              0.004791847               0.00160523              0.003440115              0.001532004
Gm19938              0.009784733              0.090196942               0.08589228              0.006415395              0.055674550
        KO1b__TTCAGGACACTGCTTC-1 KO1b__TTGGGTAAGATCGCTT-1 KO2b__AACAACCCAATTGCCA-1 KO2b__AACAACCCAGTCAGCC-1 KO2b__AACTTCTAGAAACTCA-1
Xkr4                 0.198393339              0.182575031             0.0064883401              0.006902564              0.011743560
Gm1992               0.001766810              0.002729809             0.0004280643              0.000321189              0.001276218
Gm19938              0.003799057              0.003728587             0.0006895850              0.000000000              0.001839424
        KO2b__AAGAACATCTCGAGTA-1 KO2b__AAGACAATCTCTGACC-1 KO2b__AAGGTAATCTCAGTCC-1 KO2b__ACAACCAGTAATTGGA-1 KO2b__ACACTGAGTCAACACT-1
Xkr4                0.0114613800             0.0084965607             0.0095982372             0.0121221555             9.186272e-03
Gm1992              0.0005441294             0.0001457142             0.0004363705             0.0006987095             9.114567e-05
Gm19938             0.0001826037             0.0001796308             0.0003241698             0.0004870753             1.608891e-04
        KO2b__ACATCGACAACCCTAA-1 KO2b__ACGTAGTGTGATATAG-1 KO2b__ACTATCTGTGATACCT-1 KO2b__ACTTCGCTCGAACGCC-1 KO2b__AGCATCAAGTTGTAGA-1
Xkr4                  0.17948307              0.009894492             0.0119213430              0.196536136             0.0070589573
Gm1992                0.02672788              0.001183222             0.0008411763              0.026334133             0.0008473279
Gm19938               0.02309038              0.080583195             0.0004582223              0.008916911             0.0009061439
        KO2b__AGGGAGTAGCCATGCC-1 KO2b__AGGTCTATCTTCGTGC-1 KO2b__AGTGCCGAGAGTTGCG-1 KO2b__AGTGTTGTCTTCCACG-1 KO2b__ATCACAGTCCGACATA-1
Xkr4                 0.016842186              0.013088133             0.0141747184              0.021592321               0.15026077
Gm1992               0.002641285              0.001060934             0.0007257499              0.003996850               0.04430205
Gm19938              0.055314172              0.001754259             0.0003838340              0.004484458               0.08114548
        KO2b__ATCAGGTAGCATCCTA-1 KO2b__ATGTCTTAGGGTTGCA-1 KO2b__ATTACTCGTTTCGTGA-1 KO2b__ATTCCTACACGTCATA-1 KO2b__ATTCTTGGTAATGCGG-1
Xkr4                4.182783e-03             0.0043853994              0.015614263               0.10021208              0.013735564
Gm1992              8.914081e-05             0.0000643153              0.003072235               0.01179785              0.001710268
Gm19938             4.024107e-04             0.0004786439              0.073160981               0.01815680              0.063916326
        KO2b__ATTGTTCCACCCTAGG-1 KO2b__ATTGTTCTCATGGAGG-1 KO2b__CAATACGAGATGCGAC-1 KO2b__CATGCTCTCCCTAGGG-1 KO2b__CCACAAACATACAGGG-1
Xkr4                 0.007227872              0.019466246               0.03207303             0.0180907610              0.019720766
Gm1992               0.000212590              0.003253408               0.00439240             0.0007439243              0.001744351
Gm19938              0.000342646              0.062619085               0.06446691             0.0000000000              0.055757996
        KO2b__CCATAAGAGGCTTTCA-1 KO2b__CCATAAGGTGACAGCA-1 KO2b__CCCGAAGAGAATTCAG-1 KO2b__CCCGGAACACAAAGTA-1 KO2b__CCGATCTCATCATCCC-1
Xkr4                  0.01046499              0.014688649              0.021898681              0.013866350             0.0302781172
Gm1992                0.00122690              0.002873305              0.001216872              0.002335319             0.0015322846
Gm19938               0.05466726              0.072751015              0.001741371              0.069296779             0.0002191857
        KO2b__CCGGACATCTTTGGAG-1 KO2b__CCTCTAGTCGACCTAA-1 KO2b__CGAGGCTGTCGTCGGT-1 KO2b__CGATCGGGTAATGATG-1 KO2b__CGTTGGGCAAGCAGGT-1
Xkr4                0.0144293828              0.013717429             0.0056561514             0.0372748404             0.0071706770
Gm1992              0.0004103346              0.002274577             0.0001685468             0.0027077965             0.0004871271
Gm19938             0.0000000000              0.068575303             0.0005777598             0.0006185945             0.0012072372
        KO2b__CTAGGTAAGTGCTAGG-1 KO2b__CTCCATGTCTTACGTT-1 KO2b__CTCCGATTCCGAGATT-1 KO2b__GAATAGAAGGTTCCGC-1 KO2b__GACCTTCGTCCGACGT-1
Xkr4                 0.011706906              0.018809668             4.907989e-03              0.037235876               0.01293543
Gm1992               0.001055139              0.001508032             6.468331e-05              0.003108438               0.00248553
Gm19938              0.060909458              0.049640071             1.759663e-04              0.053094305               0.06919154
        KO2b__GCTACCTAGTTGCTCA-1 KO2b__GGAAGTGTCGCTAGCG-1 KO2b__GGAGATGCATTGCCTC-1 KO2b__GGAGATGTCTCTATGT-1 KO2b__GGAGGTAGTAGTTAGA-1
Xkr4                 0.015000700              0.016039012              0.024582704              0.021310057              0.056812768
Gm1992               0.002310246              0.002629133              0.002986267              0.001670585              0.013777051
Gm19938              0.062645436              0.060780061              0.003187708              0.002410319              0.005733195
        KO2b__GGCAGTCCAAGAGAGA-1 KO2b__GGGATGATCGAGATAA-1 KO2b__GGGTCTGGTCGCGTCA-1 KO2b__GGTCACGGTTCGGCCA-1 KO2b__GGTGATTCATTAGGCT-1
Xkr4                0.0054204574              0.047489478              0.007514545             0.0069506861             0.0112377332
Gm1992              0.0006418359              0.005102033              0.001076306             0.0001335090             0.0004798078
Gm19938             0.0006588986              0.048433616              0.001112176             0.0006168647             0.0000000000
        KO2b__GGTTCTCTCTGGGTCG-1 KO2b__GTAAGTCGTCGGAACA-1 KO2b__GTCACTCAGCAGTCTT-1 KO2b__GTGCTGGAGCATGTTC-1 KO2b__TAATTCCAGCTCACTA-1
Xkr4                0.0107863347              0.010550438             0.0112334117             0.0118612932              0.067980530
Gm1992              0.0006339265              0.001076289             0.0005430852             0.0005738641              0.005885857
Gm19938             0.0015961262              0.050587332             0.0000000000             0.0010332242              0.046866043
        KO2b__TACCCGTCAAGTGGGT-1 KO2b__TACCTCGTCCTTCTGG-1 KO2b__TATCAGGAGGGTAGCT-1 KO2b__TATCTGTTCCGGGACT-1 KO2b__TATGTTCCACGTAGAG-1
Xkr4                 0.019872330             0.0118208806             0.0226261714             0.0219771792             0.0051086646
Gm1992               0.001368075             0.0005978684             0.0012093241             0.0010835017             0.0001659014
Gm19938              0.063615490             0.0002894600             0.0001223756             0.0002253995             0.0005753697
        KO2b__TATTGGGAGTCTCCTC-1 KO2b__TCACGCTGTGCATCTA-1 KO2b__TCAGTCCCAGCGGTTC-1 KO2b__TCATATCAGACCTGGA-1 KO2b__TCATGAGTCTGAATCG-1
Xkr4                0.0172095814             0.0194322360              0.024697258              0.107701126             7.383872e-03
Gm1992              0.0019475471             0.0010541112              0.004088947              0.010382650             1.166523e-04
Gm19938             0.0001601402             0.0007608382              0.076498231              0.002836221             6.574768e-05
        KO2b__TCATGCCTCATCGGGC-1 KO2b__TCCATCGGTACAACGG-1 KO2b__TCCCATGCATTCTGTT-1 KO2b__TCGACGGTCTCTATGT-1 KO2b__TCGGGCACACACAGCC-1
Xkr4                0.0060019916             0.0172806512             0.0132368773             0.0173117830             0.0128574965
Gm1992              0.0002355322             0.0003396783             0.0009203725             0.0008438032             0.0008775744
Gm19938             0.0001421236             0.0002329882             0.0525409113             0.0002852165             0.0717542414
        KO2b__TGACGCGAGACTCGAG-1 KO2b__TGAGGTTAGTGGTCAG-1 KO2b__TGAGTCAAGATTACCC-1 KO2b__TGCTGAACAGAGAATT-1 KO2b__TGTAACGCATACACCA-1
Xkr4                0.0157483457             0.0152462046              0.023073569               0.14563266             0.0242661648
Gm1992              0.0009351966             0.0008899796              0.003369802               0.01529307             0.0021314828
Gm19938             0.0453163107             0.0013052136              0.003843975               0.00537815             0.0001460835
        KO2b__TGTACAGGTACAGCGA-1 KO2b__TGTCCACTCTCGTGGG-1 KO2b__TGTGAGTAGCTTCTAG-1 KO2b__TGTGATGCACTGTGAT-1 KO2b__TGTTGGACAACTCCAA-1
Xkr4                 0.013334434             0.0115781913              0.015321507             5.755430e-03              0.023630443
Gm1992               0.003027462             0.0005244177              0.001127139             2.411342e-04              0.002349911
Gm19938              0.091494402             0.0001816813              0.061854255             2.828841e-05              0.004058581
        KO2b__TTAGGCAGTAGACAAT-1 KO2b__TTCCGTGCACTTCAGA-1 KO2b__TTCTAACCATACCATG-1 KO2b__TTGAGTGGTAGCTTGT-1 KO2b__TTGGGATAGCAACCAG-1
Xkr4                0.0089766109             0.0116076807              0.029312658              0.014376061             4.147492e-03
Gm1992              0.0002123448             0.0009502741              0.004287077              0.002586647             5.128036e-05
Gm19938             0.0002336707             0.0017779999              0.069365733              0.002517031             1.992780e-04
        KO2b__TTGTGGAGTCAAAGCG-1 KO2b__TTTACGTGTACCCGAC-1 WT1b__AAGACAAGTTCGTGCG-1 WT1b__ACAAAGAAGAGGTTTA-1 WT1b__ACATCGAGTCGAATGG-1
Xkr4                 0.013902896              0.024022177             1.646549e-01             0.1290224053               0.16303013
Gm1992               0.002215252              0.001789123             6.078757e-02             0.0244409189               0.02973493
Gm19938              0.065173815              0.056832571             3.849511e-05             0.0001952056               0.00000000
        WT1b__ACGATGTGTCACGCTG-1 WT1b__ACGTCCTCATGACTGT-1 WT1b__AGGGCTCCAGAGGCTA-1 WT1b__AGGGCTCTCGTGGGAA-1 WT1b__AGTGATCCAATTGCGT-1
Xkr4                 0.157017587             0.1401755523             0.1558497329              0.181968299               0.18189955
Gm1992               0.012181778             0.0242349976             0.0490933529              0.060471179               0.06459732
Gm19938              0.002789195             0.0005143528             0.0004898991              0.002395378               0.00000000
        WT1b__ATATCCTGTAGCTCGC-1 WT1b__ATCACAGAGTGAGGTC-1 WT1b__ATCGTGACAGGAGGTT-1 WT1b__ATGAGTCAGCTCGGCT-1 WT1b__ATGCATGGTGTCTTAG-1
Xkr4                 0.171136274             0.1817991054             0.1376464014              0.172001721               0.19618258
Gm1992               0.039122145             0.0672830556             0.0367951344              0.051406809               0.05484993
Gm19938              0.001526935             0.0002943152             0.0006772085              0.003633916               0.00000000
        WT1b__ATTGTTCGTGTCCAAT-1 WT1b__ATTTCACGTAGGTTTC-1 WT1b__ATTTCTGGTTCAAGGG-1 WT1b__CAAGACTTCATCTCTA-1 WT1b__CAATTTCCAGTCGGTC-1
Xkr4                 0.230953346               0.15396519             1.781602e-01             1.792875e-01             0.1769434771
Gm1992               0.017169332               0.07871305             6.434000e-02             9.207454e-02             0.0703607334
Gm19938              0.002319848               0.00000000             4.272497e-05             6.398278e-05             0.0008794827
        WT1b__CACGTTCCAACCACAT-1 WT1b__CAGAGCCGTGCATTTG-1 WT1b__CAGTTAGGTCGTGGTC-1 WT1b__CATTCTACATACCATG-1 WT1b__CCCTTAGCAGCGCTTG-1
Xkr4                 0.180386767              0.221433494               0.13274141              0.217089833              0.166089747
Gm1992               0.024405294              0.049395451               0.03597625              0.026636569              0.063044329
Gm19938              0.001415537              0.006689287               0.00000000              0.002227293              0.002359146
        WT1b__CCGAACGGTATGGTTC-1 WT1b__CCGATCTTCGACACCG-1 WT1b__CCGATGGAGGGTTAAT-1 WT1b__CCGGTAGGTACCCACG-1 WT1b__CCTTCAGCACGCGTGT-1
Xkr4                 0.269204220              0.160546840              0.134452016               0.16423313             1.614157e-01
Gm1992               0.046923636              0.041544564              0.038699870               0.04640784             6.129539e-02
Gm19938              0.005692199              0.005328112              0.002772388               0.00000000             3.608626e-05
        WT1b__CGCATAATCCACACCT-1 WT1b__CGTCAAAAGGAAAGGT-1 WT1b__CTCCAACTCGAGAATA-1 WT1b__CTGCCATCAGAGGCAT-1 WT1b__CTGGACGTCTCCCATG-1
Xkr4                 0.148545277             1.386115e-01             0.1564848540               0.14162349               0.18857230
Gm1992               0.020706247             2.391882e-02             0.0227482565               0.04970115               0.05272873
Gm19938              0.000461769             4.782714e-05             0.0006512869               0.00000000               0.00000000
        WT1b__CTGTACCCAAGATGTA-1 WT1b__GAAGTAAGTACACTCA-1 WT1b__GACATCATCCTATTGT-1 WT1b__GACTATGCATGACTTG-1 WT1b__GAGAAATGTTCGGACC-1
Xkr4                  0.14512015             0.1530511003               0.22495570               0.15361591               0.13649278
Gm1992                0.03972248             0.0245450638               0.07361688               0.04318013               0.01577851
Gm19938               0.00233019             0.0002177483               0.01253897               0.00000000               0.00021732
        WT1b__GAGAGGTAGATCCAAA-1 WT1b__GAGTGAGTCACTGTCC-1 WT1b__GCAACATCACGATTCA-1 WT1b__GCCAGCAGTCGGTGAA-1 WT1b__GGAATGGCAGCTTTGA-1
Xkr4                1.521219e-01             0.1469699153             0.1598766940              0.171606810             0.1566266194
Gm1992              2.533257e-02             0.0369683664             0.0401068983              0.052734222             0.0139064809
Gm19938             6.785663e-05             0.0002794742             0.0001767062              0.001032217             0.0007144675
        WT1b__GGGTAGAGTGCAGATG-1 WT1b__GGGTGTCCAGGCCCTA-1 WT1b__GGTTGTAAGGTTCTAC-1 WT1b__GTAGATCCACTCCGAG-1 WT1b__GTCAGCGAGTCGCGAA-1
Xkr4                 0.189630656              0.159355228             0.1752783245               0.15204926               0.22634272
Gm1992               0.059495572              0.040282346             0.0590018084               0.05424689               0.08161533
Gm19938              0.000528568              0.000368075             0.0006592593               0.00000000               0.00000000
        WT1b__GTGCACGTCATTGTTC-1 WT1b__GTTACAGGTCAACCAT-1 WT1b__TACTTACGTCTTCATT-1 WT1b__TACTTCATCCTCAGAA-1 WT1b__TACTTGTGTTTGGGAG-1
Xkr4                 0.227953501             1.685515e-01               0.16184651             1.820910e-01             0.1370153803
Gm1992               0.024638356             4.045465e-02               0.04461507             7.193871e-02             0.0275210066
Gm19938              0.004133847             6.322076e-05               0.00000000             4.722692e-05             0.0001916854
        WT1b__TCACACCCATCGCTAA-1 WT1b__TCCCATGTCGCTACGG-1 WT1b__TCCTCGAAGGTGATAT-1 WT1b__TCTGGCTCAACTTGCA-1 WT1b__TGAGGTTCAGTGGGTA-1
Xkr4                 0.203031521               0.17290720             0.1406176901             0.1539730773              0.247799394
Gm1992               0.013336785               0.07240661             0.0257442197             0.0497823140              0.056076458
Gm19938              0.007558264               0.00000000             0.0000772036             0.0001658452              0.008121969
        WT1b__TGCAGATTCACCTACC-1 WT1b__TGCGGGTTCCGCGGAT-1 WT1b__TGGGCTGAGAGCCGTA-1 WT1b__TGGGCTGAGTAGGGTC-1 WT1b__TGTTGGATCTAGTCAG-1
Xkr4                0.1508612393             1.639839e-01             0.1806919306              0.142448863             1.597979e-01
Gm1992              0.0177092480             2.176841e-02             0.0686743279              0.041520014             2.395921e-02
Gm19938             0.0007943497             6.678226e-05             0.0001492095              0.001214155             6.074446e-05
        WT1b__TTTCAGTCAACACAAA-1 WT1b__TTTCAGTTCGCGATCG-1 WT2b__AAACCCATCCAAGCTA-1 WT2b__AAACGAACACAGTGAG-1 WT2b__AAAGAACAGCGTCGAA-1
Xkr4                 0.186763478                0.1708012             0.1101806528             0.0405067359              0.073485720
Gm1992               0.040419811                0.0595273             0.0026557883             0.0001081337              0.008846645
Gm19938              0.003467035                0.0000000             0.0002106173             0.0000000000              0.001139166
        WT2b__AAAGGATAGCCACAAG-1 WT2b__AAAGGTACACAGCCAC-1 WT2b__AAAGGTAGTGTCGCTG-1 WT2b__AAATGGATCTCTCGAC-1 WT2b__AACGAAAGTCTGGTTA-1
Xkr4                8.116344e-02             0.0837629550             1.252232e-01             0.0375782707              0.098186368
Gm1992              8.346572e-04             0.0046712354             5.425813e-05             0.0001699182              0.023136080
Gm19938             2.032004e-05             0.0007721834             0.000000e+00             0.0000000000              0.006239731
        WT2b__AAGGAATTCCATTGCC-1 WT2b__AAGTCGTTCCATGAGT-1 WT2b__AATCGACGTAATTAGG-1 WT2b__AATGAAGCACAAATAG-1 WT2b__ACACAGTCAGACAATA-1
Xkr4                 0.082512698             0.1250107370               0.46138356              0.122088781             0.0929754940
Gm1992               0.031413493             0.0004551815               0.09479826              0.002282249             0.0025696361
Gm19938              0.004474241             0.0000000000               0.04518340              0.000124799             0.0001037049
        WT2b__ACACGCGGTCGTAATC-1 WT2b__ACATCGACAGCCGTTG-1 WT2b__ACATGCACACAAGTTC-1 WT2b__ACTATGGAGCGTCAAG-1 WT2b__ACTTTGTCAGCTGCCA-1
Xkr4                0.0667408690             1.271932e-01             0.0703923904             7.104427e-02              0.090716639
Gm1992              0.0074075665             9.032323e-04             0.0006084107             2.209145e-03              0.000762737
Gm19938             0.0009263125             3.606439e-05             0.0000000000             7.994391e-05              0.000000000
        WT2b__AGAACCTCACGCTTAA-1 WT2b__AGAAGTAGTAGCTTGT-1 WT2b__AGACCCGCAGCTGAGA-1 WT2b__AGAGAATCATACCATG-1 WT2b__AGCATCAAGCTTTGTG-1
Xkr4                0.0757606142             0.0551128015             0.1006243192             0.1038387211              0.065575645
Gm1992              0.0005785908             0.0014785705             0.0131352039             0.0156039371              0.011515231
Gm19938             0.0000000000             0.0000402976             0.0004866938             0.0006200897              0.000358695
        WT2b__AGGAATACATCCCGTT-1 WT2b__AGGATAACAACTACGT-1 WT2b__AGTACTGTCGAACTCA-1 WT2b__AGTGCCGAGGACACTG-1 WT2b__ATACCTTGTGATCGTT-1
Xkr4                0.1075567587             8.531597e-02             4.972897e-02             0.0540579234             0.0663313679
Gm1992              0.0160415893             2.508034e-03             1.392463e-03             0.0060453630             0.0005860704
Gm19938             0.0005400691             7.200841e-05             5.457691e-05             0.0001500909             0.0000000000
        WT2b__ATCACAGAGACAAGCC-1 WT2b__ATCCGTCCAAGACGAC-1 WT2b__ATCGATGAGTGGGAAA-1 WT2b__ATCGGATCAACTGAAA-1 WT2b__ATGCATGCATCCCACT-1
Xkr4                 0.108061200             0.0607377798             0.0574643351              0.125229935             0.0711181648
Gm1992               0.008295665             0.0008436062             0.0008552665              0.026977429             0.0093447702
Gm19938              0.000611189             0.0000000000             0.0000000000              0.003617571             0.0009767108
        WT2b__ATTCATCGTCTGCCTT-1 WT2b__ATTCCCGGTGATAGTA-1 WT2b__ATTCTTGCAAGTATCC-1 WT2b__ATTTCTGAGTAACAGT-1 WT2b__ATTTCTGGTCTTGAGT-1
Xkr4                 0.091265475             0.0519243243             0.0428375663             0.0474451452             0.0587990652
Gm1992               0.003374706             0.0004120392             0.0002693457             0.0001337902             0.0003494119
Gm19938              0.001064393             0.0000000000             0.0000000000             0.0000000000             0.0000000000
        WT2b__CAAGACTGTCCAAAGG-1 WT2b__CACAACATCTGTGCTC-1 WT2b__CACCGTTTCGTCCTCA-1 WT2b__CAGATACTCATACGAC-1 WT2b__CAGCACGCACAAGCTT-1
Xkr4                 0.070892947             0.0467255274              0.109770082              0.063019460             0.0511608451
Gm1992               0.012388116             0.0001918672              0.016490239              0.000135037             0.0003230142
Gm19938              0.000639592             0.0001618528              0.000723887              0.000000000             0.0005632297
        WT2b__CATCCACCAAAGGCAC-1 WT2b__CATCCCAGTGGCCTCA-1 WT2b__CATGCAATCATTACTC-1 WT2b__CATTCCGTCCAAGCAT-1 WT2b__CCACGAGTCTATTGTC-1
Xkr4                 0.064237568             0.0666097014             0.0599197244              0.177881917             0.0496084959
Gm1992               0.004626065             0.0032047794             0.0007395185              0.045014344             0.0001689539
Gm19938              0.000000000             0.0001308799             0.0000000000              0.006109584             0.0000000000
        WT2b__CCACGTTTCGGCGATC-1 WT2b__CCTCAGTTCCCAACTC-1 WT2b__CCTCATGCAAATACGA-1 WT2b__CGAATTGAGATACCAA-1 WT2b__CGATGGCGTAGGGTAC-1
Xkr4                 0.064717517             8.272891e-02              0.052943087             0.0634230223             8.761164e-02
Gm1992               0.002990724             3.677355e-03              0.000579128             0.0068263499             3.572088e-03
Gm19938              0.000000000             6.694369e-05              0.000000000             0.0001956359             7.909124e-05
        WT2b__CGCAGGTGTATCTCGA-1 WT2b__CGCGTGAAGAATTGCA-1 WT2b__CGGGCATGTAGGTGCA-1 WT2b__CGGGTCAAGGGCTTCC-1 WT2b__CGTGAATCACCGTACG-1
Xkr4                0.0532199309              0.061876917             0.1506083299             0.0630460014             0.0667802330
Gm1992              0.0004519242              0.000187046             0.0103022077             0.0002140972             0.0003940656
Gm19938             0.0000000000              0.000000000             0.0004855724             0.0000000000             0.0000000000
        WT2b__CGTGATACAGTGACCC-1 WT2b__CTCAATTTCGTGGACC-1 WT2b__CTCATGCCAATAGGGC-1 WT2b__CTCATTACATGGCCCA-1 WT2b__CTCCCAACAGAGTGAC-1
Xkr4                0.0575492430              0.090249651             0.1137118857             0.0739524924              0.137043141
Gm1992              0.0086695597              0.025914142             0.0029640430             0.0081936665              0.012952110
Gm19938             0.0003119189              0.003077991             0.0001332006             0.0008108654              0.001240238
        WT2b__CTGCCTAAGCTGACTT-1 WT2b__CTTAGGATCTTACGGA-1 WT2b__CTTCCGATCGTTGTGA-1 WT2b__GAAGCGATCCGGCAAC-1 WT2b__GAAGTAATCGACGATT-1
Xkr4                 0.093405303             7.657515e-02             0.0555418924             7.889708e-02             7.400611e-02
Gm1992               0.015304995             3.381693e-03             0.0010293733             1.371194e-03             3.926957e-03
Gm19938              0.001702276             5.471768e-05             0.0001558714             1.878412e-05             8.061993e-05
        WT2b__GAATAGAGTTGTCTAG-1 WT2b__GAATCACCACGCACCA-1 WT2b__GACGCTGCACCTGAAT-1 WT2b__GAGCCTGCAAAGGGCT-1 WT2b__GAGGGTAGTCGCATGC-1
Xkr4                0.0732573019             0.0918587000             0.0797094629             7.044031e-02             0.0677060138
Gm1992              0.0005690062             0.0030166958             0.0078903960             1.067593e-03             0.0066535185
Gm19938             0.0000000000             0.0002663344             0.0001984022             5.131651e-05             0.0001127723
        WT2b__GATCACAGTACAGCGA-1 WT2b__GCAGCTGCACGCCACA-1 WT2b__GCATCTCCACGGATCC-1 WT2b__GCCAGGTGTGAGTGAC-1 WT2b__GCGGATCGTTGGGTAG-1
Xkr4                 0.074666427             0.0607983866             0.1242276111             0.0702558616             0.0417635143
Gm1992               0.009741923             0.0048738240             0.0085179240             0.0002933926             0.0002026119
Gm19938              0.001324735             0.0001654709             0.0005735404             0.0000000000             0.0000000000
        WT2b__GGAGAACTCTGCGGAC-1 WT2b__GGGCCATGTGGGACAT-1 WT2b__GGTAATCCAGCGATTT-1 WT2b__GTAGCTATCCCGAGAC-1 WT2b__GTAGGTTAGGAAAGGT-1
Xkr4                 0.113857707             0.0865889411             6.345203e-02             0.0636006961             0.0427208016
Gm1992               0.001477447             0.0037667132             2.990471e-03             0.0007867783             0.0005654534
Gm19938              0.000000000             0.0009766783             8.929586e-05             0.0000000000             0.0001925591
        WT2b__GTCAAGTGTCGTGGAA-1 WT2b__GTCACGGAGTTGGACG-1 WT2b__GTCGCGAGTAATGATG-1 WT2b__GTGGCGTGTCCAGAAG-1 WT2b__GTGGTTAAGACAGCTG-1
Xkr4                0.0623038753             0.0626618996             0.0636661389              0.073520956             0.0707930013
Gm1992              0.0132018156             0.0005525977             0.0054642137              0.019941420             0.0004461076
Gm19938             0.0004510134             0.0000000000             0.0001349265              0.002529368             0.0000000000
        WT2b__GTGGTTACACTGTTCC-1 WT2b__GTTGAACCAGTCGAGA-1 WT2b__GTTGTAGCAAGCTGCC-1 WT2b__TACCTCGGTGACACGA-1 WT2b__TATACCTAGAGCTGCA-1
Xkr4                9.613244e-02             0.0639709114             8.624245e-02             0.0646091471             0.0782283494
Gm1992              1.438237e-03             0.0001921428             1.016986e-03             0.0005621791             0.0042548486
Gm19938             8.753315e-05             0.0000000000             4.398725e-05             0.0000000000             0.0001150748
        WT2b__TATCGCCGTTTGAACC-1 WT2b__TATTGCTAGTAACGAT-1 WT2b__TCAGTCCAGCAAGCCA-1 WT2b__TCAGTTTGTACCTGTA-1 WT2b__TCATGGACAGTAGTTC-1
Xkr4                0.1011179755              0.136479262             0.0641076155             0.0534451495             0.0662318448
Gm1992              0.0026414404              0.004379611             0.0001393604             0.0066187495             0.0007691065
Gm19938             0.0001244014              0.000000000             0.0000000000             0.0001086269             0.0000000000
        WT2b__TCCGAAAGTTCGAGCC-1 WT2b__TCGATTTAGATGAAGG-1 WT2b__TCGGGACAGATGGTCG-1 WT2b__TCGTCCAAGCAATAGT-1 WT2b__TCGTGGGGTCTTTCAT-1
Xkr4                 0.126273194             0.0650380723             0.0764431523              0.075889843              0.093427577
Gm1992               0.001123515             0.0093471657             0.0006431874              0.004984067              0.015187416
Gm19938              0.000000000             0.0003083069             0.0000000000              0.001134694              0.001285635
        WT2b__TCTATACAGCTAATCC-1 WT2b__TCTCAGCCAAGTCGTT-1 WT2b__TCTCTGGTCGAGTACT-1 WT2b__TCTTAGTAGGAGTACC-1 WT2b__TGAACGTCATCCGTTC-1
Xkr4                   0.1281508             0.0761603547             0.0415716956             5.236741e-02             0.0877331443
Gm1992                 0.0015032             0.0003381642             0.0003480954             4.792393e-03             0.0046610424
Gm19938                0.0000000             0.0000000000             0.0002647004             7.556148e-05             0.0008203238
        WT2b__TGAGCGCAGGTAAGGA-1 WT2b__TGATGGTGTTAAGACA-1 WT2b__TGCCGAGCACTGAATC-1 WT2b__TGGTGATGTGAGTAAT-1 WT2b__TGTAAGCGTCCTGGTG-1
Xkr4                0.0868605868             0.0731851092             8.714473e-02              0.072245603             8.225725e-02
Gm1992              0.0008600709             0.0006452647             1.151104e-03              0.010358461             6.091631e-05
Gm19938             0.0000000000             0.0000000000             2.583286e-05              0.001241175             0.000000e+00
        WT2b__TTAGGGTGTCCGGTCA-1 WT2b__TTCAGGACAGAGTCAG-1 WT2b__TTCAGGATCCAATCTT-1 WT2b__TTCCTCTGTAGTCTGT-1 WT2b__TTCTAGTCACCTTCGT-1
Xkr4                0.0693800578              0.074028842             0.0674754947              0.067894342             0.0951929732
Gm1992              0.0098312448              0.003407022             0.0076039067              0.007451819             0.0027714499
Gm19938             0.0002549284              0.000000000             0.0002046985              0.000227541             0.0001503651
        WT2b__TTCTAGTGTTAAGCAA-1 WT2b__TTCTTGACAGGTGTGA-1 WT2b__TTGTTGTCATGGGTCC-1 WT2b__TTGTTTGTCAAGAGTA-1 WT2b__TTTCGATGTTAGGAGC-1
Xkr4                 0.086990947              0.071425504             0.0675078750               0.04815164             0.0752564017
Gm1992               0.026279684              0.000724951             0.0005059081               0.00119762             0.0007959253
Gm19938              0.003621121              0.000000000             0.0000000000               0.00000000             0.0000000000
        WT2b__TTTGTTGAGAATCTAG-1
Xkr4                  0.09512820
Gm1992                0.00210776
Gm19938               0.00000000

This is the assay of imputed-normalized data by Magic. The problem appear when I try to run SetdatExpr():

seurat.integrated <- SetupForWGCNA(
   seurat.integrated,
   gene_select = "fraction",
   fraction = 0.05,  
   wgcna_name = "endothelial" # the name of the hdWGCNA experiment
 )

#  # construct metacells  in each group
 seurat.integrated <- MetacellsByGroups( seurat_obj = seurat.integrated, assay = "MAGIC_RNA", reduction = "umap",
   group.by = c("integrated_snn_res.0.1", "condition"), # specify the columns in seurat.integrated@meta.data to group by
   k = 10, # nearest-neighbors parameter,
   min_cells = 10,
   max_shared = 10, # maximum number of shared cells between two metacells
   ident.group = 'integrated_snn_res.0.1' # set the Idents of the metacell seurat object
 )
gc()
 #  # normalize metacell expression matrix:
 seurat.integrated <- NormalizeMetacells(seurat.integrated)
seurat.integrated <- SetDatExpr(
seurat.integrated,
group_name = "17", 
group.by='integrated_snn_res.0.1', 
assay = 'MAGIC_RNA', # using RNA assay
slot = 'data' # using normalized data)

Error in WGCNA::goodGenes(datExpr, ...) : 
  Too few genes with valid expression levels in the required number of samples.

Can u help me to figure out how to handle with a so-low expression values due to the imputation?

smorabit commented 1 month ago

It seems like this is a problem with MAGIC not with hdWGCNA , so I am not sure if I can help you. I recommend trying to run hdWGCNA as suggested in the tutorial rather than using MAGIC imputed data.

smorabit commented 1 month ago

Closing due to inactivity.