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DavisLaboratory / singscore

An R/Bioconductor package that implements a single-sample molecular phenotyping approach
https://davislaboratory.github.io/singscore/
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Error in "generateNull" #15

Closed hyojin0912 closed 4 years ago

hyojin0912 commented 4 years ago

Hello

I am a student studying at KAIST in South Korea.

First, thank you for nice package.

I want to use singscore for enriching immune cell type specific genes.

But I got error when generate Null distribution.

By experiment, I realized that generateNull print "Error in quickdf(unname(split(vec, rep(seq_len(ncol), nrow)))) :

length(rows) == 1 is not TRUE" when generating null distribution using only upSet.

image

ruqianl commented 4 years ago

Hi @hyojin0912 ,

I think it is due to that generateNull currently only takes one GeneSet, so if you have a list of GeneSets, you could generate a Null distribution for each one of them for now.

hyojin0912 commented 4 years ago

Thanks for your kind reply. But I got same error even if I use single gene set.

image

Could you run with my data and get output of p value per sample?

I would attach files I used test.txt

ruqianl commented 4 years ago

Hi @hyojin0912 ,

Did you check the gene ids in the gene set is matching the rownames in you exp_sym? could you share that file (exp_sym) too? so I can reproduce the error to find an easiest way that will work for you.

Thanks

hyojin0912 commented 4 years ago

Okay thanks for your help. I upload gene expression matrix (exp_sym.txt) which is gene symbol by sample preprocessed matrix. Then, Immune Gene Set matrix (Immune Gene Set.txt) which is gene set using gene symbol. Each column is gene set then, I want to get score per gene set per sample. exp_sym.txt https://drive.google.com/file/d/1IS201GJ1gapzhc9oTskCKQPbUBjOWKQm/view?usp=drive_web

Best regards

Hyojin Son Synergistic Bioinformatics Lab http://synbi.kaist.ac.kr/ Korea Advanced Institute of Science and Technology 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea Office: Room #411, CMS Building (E16) TEL: +82-42-350-4358 CP: +82-10-4431-0884 E-mail: hyojin0912@kaist.ac.kr

2019년 9월 27일 (금) 오후 1:33, Rachael-rq notifications@github.com님이 작성:

Hi @hyojin0912 https://github.com/hyojin0912 ,

Did you check the gene ids in the gene set is matching the rownames in you exp_sym? could you share that file (exp_sym) too? so I can reproduce the error to find an easiest way that will work for you.

Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DavisLaboratory/singscore/issues/15?email_source=notifications&email_token=AJKE5VZ26SXTPBXD2E5EF2LQLWEKTA5CNFSM4IZMQ5MKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7XWAXY#issuecomment-535781471, or mute the thread https://github.com/notifications/unsubscribe-auth/AJKE5VYAMHIAT7UELXDDFCLQLWEKTANCNFSM4IZMQ5MA .

All T cells CD8+T cells T regulatory cells B cells Resting NK cells Classical monocytes Intermediate monocytes Nonclassical monocytes Mature DC’s Monocyte-derived DC’s Mature neutrophils Immature neutrophils CD3G FCGBP AKAP2 PSEN2 IL18RAP S100A12 GFRA2 C1QA ACCL5 CD1A ALPL AZU1 CD3D C1ORF21 ANXA2 FZD5 PRF1 ALOX5AP NKG7 HES4 CXCL10 CD1B IL8RB ELA2 TRA PHEMX C8FW PLEKHF2 GZMH PAD14 PLVAP CDKN1C CCR7 CD1C FCGR3B BPI CD6 KLRG1 CALM2 SIDT2 TKTL1 NRG1 PLAC8 C1QB IL15 CD23A SEMA3C LCN2 CD5 ZNF145 CDH13 MTPN MCEMP1 MARCKSL1 RHOC IF127 MRC1 HM74 MPO NPDC1 ADRB2 ENTPD1 TUBB6 THBS1 E2F2 CLEC4F IF144L CD36 SOD2 CTSG CD28 DUSP2 EPSTI1 FLJ21127 CRISPLD2 G8P4 ADA IFIH1 HLA-DQA FCGR3A MMP8 CAMK4 IL2RB F5 SMC6L1 F13A1 CLEC10A TAGLN IFIT1 HLA-B IL-8 DEFA4 GFI1 CCL5 GBP2 KIAA1026 MOSC1 SCD TCF7L2 MX1 RIL STHM DEFA3 GATA3 GZMC GBP5 NUP88 CYP27A1 COTL1 CD798 ISG15 RAP1GAP IL8RA CAMP SH2D1A TBX21 HS3ST3B1 GNA12 CD163 SLC29A1 CTSL ISG20 CCND2 FCGR2A X-CGD TRB CCL4L HSPCA RNTRE QPCT DDIT4 SFTPD IRF7 DUSP5 CSF3R
TNFRSF25 GZMH ICA1 GSTZ1 ADAM19 TGM2 ABI3 GBP4 PPIC NCF2
NK4 PRF1 LAIR2 RFX5 ASGR2 LILRA3 SETBP1 DUSP5 STAC AOAH
TACTILE GNLY LGALS3 XYLT1 RNASE4 ATF5 FGFRL1 NFKB1A PRKACB
BCL11B CST7 LOC51191 GL012 ALDH1A1 GPA33 CD798 ATF3 TRIB2
CD3E GPR56 MKP-7 EPB41L2 EDG3 C1QC SPRED1 TNFSF10 SHB
INPP4B KLRC1 NINJ2 LOC51760 PROK2 EVA1 SNFT IL6
MAL S100B P53DINP1 SCRN1 CLEC4D MERTK EVL IL8
NPDC1 D12S2489E PMAIP1 PTD008 S100A9 MGLL MTSS1 IL7R
ITM2A CD8B1 PTPLA CYB561D2 OSM DDEFL1 SH2D1B CCL4
ITK CD8A GPR2 SCAP2 CSPG2 MARCO CYFIP2 TNFA1P6
LCK HLA-DMA MMP11 GALS2 NR1H3 NELF IFIT3
NFATC3 HLA-DPA1 ERDJ5 ANG FBP1 STS-1 OASL
RORA HLA-DPB1 TTC7A VNN2 ACP2 SIGLEC10 GBP1
MGC19764 HLA-DQB1 PMAIP1 EBI2 GBP1 CKS1B HES4
TCF7 HLA-DRA GARNL4 UTS2 GPBAR1 PTP4A3 CYP27B1
ZAP70 HLA-DRB4 TMEPAI RPPH1 SASH1 LYPD2 RIPK2
LEF1 HLA-DRB5 SH3BP5 MGST1 OLFM1 SIDT2 TNFRSF9
SPOCK2 HPGD EDD IL8 TIMP1 INSIG1 SOD2
PRKCQ PTT1 UCP4 CCR2 HLA-DOA LTB CD38
SATB1 SAT EVI5L SELL CAMK1 PAPSS2 CD44
RASGRP1 SHMT2 PIK3C2B DYSF POUFUT1 ABCC3 CD80
LRIG1 TMOD3 SMAD3 MT1F EPB4IL3 CASP5 CD83
DPP4 TNFRSF6 LHFPL2 CD14 H19 VOM1 CD86
CD3Z VIL2 LOC57228 RANSE6 ZNF703 HSPB1 INDO
PDE4D LRRC32 GM2A CSF3R SNX5 GNGT2 MT2A
FYN CHAC1 HRK STAB1 CLEC10 HMOX1 TRAF1
WWP1 EGR1 ZNF207 CYP1B1 AK-ALPHA-1 RRAS GADD45B
LAT PYCR1 LOC92497 ADHFE1 DPB1 RNF122 MT1M
DUSP16 IL13 F5 PLA2G7 DHRS9 CDH23 MTIP2
KIAA0748 C3AR1 DMXL1 MMP25 MTHFD2 FMNL2 BIRC3
CDR2 ZBED2 CLIC4 ZNF395 RGL1 RGS12 USP18
STAT4 IL10 PRCP SLC2A3 PRDM1 SGGB3A1 TUBB2A
FLT3LG GAB3 DKFZP434C0328 EGR1 FADS1 FER1L3 CCL8
IL6ST NR4A1 STRBP CMTM2 SLC2A8 CALML4 EBI3
IL1R2 PHF16 CD9 CSK IFITM3 IFITM1
ULBP1 JUP ISOC2 CKB MT1B
IL17F TEAD2 CD300C CEACAM3 MT1E
EIF4EBP1 PPP3CA FGD2 IFITM1 MT1G
RGS16 CNR2 MT1H
BCAT1 ATP5B GADD45A
VEGFA ABCA1 CD200
GIMAP1 BMF LAMP3
GPR44 ZCCHC7 RGS1
GPT2 KIAA0274 SAT1
PSPH SLC22A3
NLN SPI1
MS4A3 AMFR
UCK2 ANXA4
TNIP3 EBF
TNFRSF9 ITPR1
IL7R HIST1H2BK
NR4A3 COPS3
CSGALNA COL14A1
CT1 SAV1
SLC43A1 APOBEC3B
ZBTB32 CCNG2
SCFD2 STAG3
HK2 LOC348938
C17ORF96 POLD4
C1ORF186 TBC1D1
LYZ MK2S4
SFXN4 APG4A
CYP1B1 DAPP1
SLC7A5 TNFRSF18
C17ORF58 HERPUD1
SLC4A5 POU2F2
CD52 ADK
KLRB1 CKIP-1
S100A4 ACTA2
POLA1 PARP14
SLC7A1 MTSS1
ATPBD4 DTX1
UBXN8 DDR1
CASP8 RRAS2
FAIM3 RNF141
IL12RB2 SYPL
MPP7 SSPN
ZNF831 CORO1C
BNIP3L NFKBIE
LRP8 CHD7
UTRN SP140
SOCS3 WDR34
LY9 BTNL9
EVI2B ATP6V0A1
SFXN3 UROS
TNFRSF4 HLA-DOA
ING4 C22ORF13
BLM IFI27
TNFSF11 JMJD2B
SLFN5 WEE1
CCR8 ODC1
CD244 KIAA0746
MYO1F WDR11
HOMER1 SYNGR2
ATF3 FOXP1
AGPAT4 BLR1
CTH MYO1E
JAKMIP1 MYBL2
TFRC GYLTL1B
RPL26L1 SETBP1
MICAL1 KLF1
GPRASP1 INPPL1
TMX4 LOC54103
FYB ZNF154
ZNF792 MHC2TA
WDR4 CD24
HUWE1 ARHGEF3
CD83 BIRC3
TRIB2 TRIM56
LARP1B HLA-DPB1
SLC38A5 UVRAG
AUH CD38
CTPS PEA15
CYTH1 FLJ10697
APOL3 TLR10
CHD6 ARHGAP10
IL1R1 HLA-DRA
LPCAT4 SHMT2
CITED2 LGALS9
DUSP4 FLJ10853
SSBP2 CEBPB
LAYN PRICKLE1
ZFAND2B LCP21
PIK3R1 CR1
GCNT4 KLHL14
PPP3CA TLR7
TIMP1 C20ORF72
SIRPG HLA-DQB2
CCR3 CORO1A
PTP4A3 PRKCE HECW2
SERINC5 FLJ25604
MAGOHB TRIM26
GIMAP4 FBXO41
KLHL24 GCNT1
CCNG2 LRMP
WDR70 UBE2J1
MYBL1 IGKV3D
CNPY4 PCCA
TIMM8A GLDC
CCDC28A CYSLTR1
MNAT1 BTLA
MS4A2 NET5
GZMB HLA-DPA1
E2F5 BLNK
HIBCH CD79B
C9ORF91 TM4SF8
NHP2 TFEB
CDC25B CD11ORF24
VDR ADRBK2
CSF1 CDKN2A
GPATCH4 RIPK2
NFKBID STX7
TMCO7 NCF4
EHBP1 SRGAP2
FAM173B SLC2A5
FARS2 CTSZ
FLVCR2 AIM2
NPM3 TCF4
PNPO TPD52
P2RY8 MAP3K8
TMEM63A MOBKL2B
MXI1 HLA-DOB
MRTO4 IFIT3
SESN2 MGC24039
C1ORF38 BRD4
STK38 RALGPS2
SLC6A6 SEMA4B
ALG14 BSG
LXN IGKC
TNFRSF18 HLA-DRB6
ACSS1 FUBP1
UBA7 UNC84B
MTSS1 IFNGR2
PSMA6 HSPA5
FAM8A1 HLA-DRB5
RAB31 MARCKS
TNRC6B KYNU
SESN1 PACAP
CEP68 RHOBTB2
LAPTM5 FLJ12363
PLAGL2 TMED8
LRRC33 FGD2
EIF2B3 FBXO10
URB2 IL4R
DDX21 CD1C
ITGA4 MGC50844
RGS2 MRPL49
RORC CTSH
IFNAR2 LYN
CSDA WASPIP
SORL1 C3ORF6
LRRC37B EGR1
IL10RA IGKV15
PRKACB SPAP1
CBWD1 CHERP
SMAD3 IGHG3
C1ORF96 ADAM28
FCER1A HLA-DMA
HSP90AB1 HLA-DMB
EMG1 PALM2-AKAP2
CD86
LAF4
LOC283663
FREB
DKFZP586A0522
UREB1
IGLL1
HLA-DQA2
KIAA1219
PLCG2
01-Mar
BCNP1
PNOC
CD20
PSCD1
BCL11A
VPS28
SWAP70
SYK
BCL7A
NAP1L
TEM6
BTK
RAB30
FCGR2B
STAT6
BRDG1
LOC201895
ITGB1
CD74
CORO2B
VPREB3
HSPC182
MGC15619
RHOH
IGHA
CYBASC3
KIAA0125
RAM2
CD83
FCRH1
FLII
SNX10
IGHG1
EPHX1
FLJ10979
GTPAP
IGLL3
E2F5
TNFRSF17
BLK
FLJ00332
SNX2
CD200
HLA-DQB1
TRIO
CYBB
PIK3AP1
IRF4
CD22
BACE2
IGJ
PAX5
RGS13
TCL1A
MEF2C
C13ORF18
POU2AF1
HHEX
IRF8
BANK1
OSBPL10
SLC2A1
NCF1
IGL@
IGLC2
SPAP1
IGHG3
HLA-DMA
HLA-DMB
CD79A
HSPA6
IGHD
KIAA0476
SLC7A7
NKG7
CD19
SAMD9
LY86
SPIB
NAPSB
RNASE6
IGHM
LY64
CD72
IRTA2
CD1D
HLA-DQA1
SAS
CTSH
LYN
WASPIP
C3ORF6
EGR1
FREB
DKFZP586A0522

hyojin0912 commented 4 years ago

Sorry, Rachael I sent wrong gene expression data I sent new one.

You can use this files

Thanks! exp_sym.txt https://drive.google.com/file/d/1IaM-Y4iXo7msqGNDZZNLlYisU_hr3s2Q/view?usp=drive_web

Best regards

Hyojin Son Synergistic Bioinformatics Lab http://synbi.kaist.ac.kr/ Korea Advanced Institute of Science and Technology 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea Office: Room #411, CMS Building (E16) TEL: +82-42-350-4358 CP: +82-10-4431-0884 E-mail: hyojin0912@kaist.ac.kr

2019년 9월 27일 (금) 오후 2:57, 손효진 sonhyojin0912@gmail.com님이 작성:

Okay thanks for your help. I upload gene expression matrix (exp_sym.txt) which is gene symbol by sample preprocessed matrix. Then, Immune Gene Set matrix (Immune Gene Set.txt) which is gene set using gene symbol. Each column is gene set then, I want to get score per gene set per sample. exp_sym.txt https://drive.google.com/file/d/1IS201GJ1gapzhc9oTskCKQPbUBjOWKQm/view?usp=drive_web

Best regards

Hyojin Son Synergistic Bioinformatics Lab http://synbi.kaist.ac.kr/ Korea Advanced Institute of Science and Technology 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Korea Office: Room #411, CMS Building (E16) TEL: +82-42-350-4358 CP: +82-10-4431-0884 E-mail: hyojin0912@kaist.ac.kr

2019년 9월 27일 (금) 오후 1:33, Rachael-rq notifications@github.com님이 작성:

Hi @hyojin0912 https://github.com/hyojin0912 ,

Did you check the gene ids in the gene set is matching the rownames in you exp_sym? could you share that file (exp_sym) too? so I can reproduce the error to find an easiest way that will work for you.

Thanks

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/DavisLaboratory/singscore/issues/15?email_source=notifications&email_token=AJKE5VZ26SXTPBXD2E5EF2LQLWEKTA5CNFSM4IZMQ5MKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD7XWAXY#issuecomment-535781471, or mute the thread https://github.com/notifications/unsubscribe-auth/AJKE5VYAMHIAT7UELXDDFCLQLWEKTANCNFSM4IZMQ5MA .

All T cells CD8+T cells T regulatory cells B cells Resting NK cells Classical monocytes Intermediate monocytes Nonclassical monocytes Mature DC’s Monocyte-derived DC’s Mature neutrophils Immature neutrophils CD3G FCGBP AKAP2 PSEN2 IL18RAP S100A12 GFRA2 C1QA ACCL5 CD1A ALPL AZU1 CD3D C1ORF21 ANXA2 FZD5 PRF1 ALOX5AP NKG7 HES4 CXCL10 CD1B IL8RB ELA2 TRA PHEMX C8FW PLEKHF2 GZMH PAD14 PLVAP CDKN1C CCR7 CD1C FCGR3B BPI CD6 KLRG1 CALM2 SIDT2 TKTL1 NRG1 PLAC8 C1QB IL15 CD23A SEMA3C LCN2 CD5 ZNF145 CDH13 MTPN MCEMP1 MARCKSL1 RHOC IF127 MRC1 HM74 MPO NPDC1 ADRB2 ENTPD1 TUBB6 THBS1 E2F2 CLEC4F IF144L CD36 SOD2 CTSG CD28 DUSP2 EPSTI1 FLJ21127 CRISPLD2 G8P4 ADA IFIH1 HLA-DQA FCGR3A MMP8 CAMK4 IL2RB F5 SMC6L1 F13A1 CLEC10A TAGLN IFIT1 HLA-B IL-8 DEFA4 GFI1 CCL5 GBP2 KIAA1026 MOSC1 SCD TCF7L2 MX1 RIL STHM DEFA3 GATA3 GZMC GBP5 NUP88 CYP27A1 COTL1 CD798 ISG15 RAP1GAP IL8RA CAMP SH2D1A TBX21 HS3ST3B1 GNA12 CD163 SLC29A1 CTSL ISG20 CCND2 FCGR2A X-CGD TRB CCL4L HSPCA RNTRE QPCT DDIT4 SFTPD IRF7 DUSP5 CSF3R
TNFRSF25 GZMH ICA1 GSTZ1 ADAM19 TGM2 ABI3 GBP4 PPIC NCF2
NK4 PRF1 LAIR2 RFX5 ASGR2 LILRA3 SETBP1 DUSP5 STAC AOAH
TACTILE GNLY LGALS3 XYLT1 RNASE4 ATF5 FGFRL1 NFKB1A PRKACB
BCL11B CST7 LOC51191 GL012 ALDH1A1 GPA33 CD798 ATF3 TRIB2
CD3E GPR56 MKP-7 EPB41L2 EDG3 C1QC SPRED1 TNFSF10 SHB
INPP4B KLRC1 NINJ2 LOC51760 PROK2 EVA1 SNFT IL6
MAL S100B P53DINP1 SCRN1 CLEC4D MERTK EVL IL8
NPDC1 D12S2489E PMAIP1 PTD008 S100A9 MGLL MTSS1 IL7R
ITM2A CD8B1 PTPLA CYB561D2 OSM DDEFL1 SH2D1B CCL4
ITK CD8A GPR2 SCAP2 CSPG2 MARCO CYFIP2 TNFA1P6
LCK HLA-DMA MMP11 GALS2 NR1H3 NELF IFIT3
NFATC3 HLA-DPA1 ERDJ5 ANG FBP1 STS-1 OASL
RORA HLA-DPB1 TTC7A VNN2 ACP2 SIGLEC10 GBP1
MGC19764 HLA-DQB1 PMAIP1 EBI2 GBP1 CKS1B HES4
TCF7 HLA-DRA GARNL4 UTS2 GPBAR1 PTP4A3 CYP27B1
ZAP70 HLA-DRB4 TMEPAI RPPH1 SASH1 LYPD2 RIPK2
LEF1 HLA-DRB5 SH3BP5 MGST1 OLFM1 SIDT2 TNFRSF9
SPOCK2 HPGD EDD IL8 TIMP1 INSIG1 SOD2
PRKCQ PTT1 UCP4 CCR2 HLA-DOA LTB CD38
SATB1 SAT EVI5L SELL CAMK1 PAPSS2 CD44
RASGRP1 SHMT2 PIK3C2B DYSF POUFUT1 ABCC3 CD80
LRIG1 TMOD3 SMAD3 MT1F EPB4IL3 CASP5 CD83
DPP4 TNFRSF6 LHFPL2 CD14 H19 VOM1 CD86
CD3Z VIL2 LOC57228 RANSE6 ZNF703 HSPB1 INDO
PDE4D LRRC32 GM2A CSF3R SNX5 GNGT2 MT2A
FYN CHAC1 HRK STAB1 CLEC10 HMOX1 TRAF1
WWP1 EGR1 ZNF207 CYP1B1 AK-ALPHA-1 RRAS GADD45B
LAT PYCR1 LOC92497 ADHFE1 DPB1 RNF122 MT1M
DUSP16 IL13 F5 PLA2G7 DHRS9 CDH23 MTIP2
KIAA0748 C3AR1 DMXL1 MMP25 MTHFD2 FMNL2 BIRC3
CDR2 ZBED2 CLIC4 ZNF395 RGL1 RGS12 USP18
STAT4 IL10 PRCP SLC2A3 PRDM1 SGGB3A1 TUBB2A
FLT3LG GAB3 DKFZP434C0328 EGR1 FADS1 FER1L3 CCL8
IL6ST NR4A1 STRBP CMTM2 SLC2A8 CALML4 EBI3
IL1R2 PHF16 CD9 CSK IFITM3 IFITM1
ULBP1 JUP ISOC2 CKB MT1B
IL17F TEAD2 CD300C CEACAM3 MT1E
EIF4EBP1 PPP3CA FGD2 IFITM1 MT1G
RGS16 CNR2 MT1H
BCAT1 ATP5B GADD45A
VEGFA ABCA1 CD200
GIMAP1 BMF LAMP3
GPR44 ZCCHC7 RGS1
GPT2 KIAA0274 SAT1
PSPH SLC22A3
NLN SPI1
MS4A3 AMFR
UCK2 ANXA4
TNIP3 EBF
TNFRSF9 ITPR1
IL7R HIST1H2BK
NR4A3 COPS3
CSGALNA COL14A1
CT1 SAV1
SLC43A1 APOBEC3B
ZBTB32 CCNG2
SCFD2 STAG3
HK2 LOC348938
C17ORF96 POLD4
C1ORF186 TBC1D1
LYZ MK2S4
SFXN4 APG4A
CYP1B1 DAPP1
SLC7A5 TNFRSF18
C17ORF58 HERPUD1
SLC4A5 POU2F2
CD52 ADK
KLRB1 CKIP-1
S100A4 ACTA2
POLA1 PARP14
SLC7A1 MTSS1
ATPBD4 DTX1
UBXN8 DDR1
CASP8 RRAS2
FAIM3 RNF141
IL12RB2 SYPL
MPP7 SSPN
ZNF831 CORO1C
BNIP3L NFKBIE
LRP8 CHD7
UTRN SP140
SOCS3 WDR34
LY9 BTNL9
EVI2B ATP6V0A1
SFXN3 UROS
TNFRSF4 HLA-DOA
ING4 C22ORF13
BLM IFI27
TNFSF11 JMJD2B
SLFN5 WEE1
CCR8 ODC1
CD244 KIAA0746
MYO1F WDR11
HOMER1 SYNGR2
ATF3 FOXP1
AGPAT4 BLR1
CTH MYO1E
JAKMIP1 MYBL2
TFRC GYLTL1B
RPL26L1 SETBP1
MICAL1 KLF1
GPRASP1 INPPL1
TMX4 LOC54103
FYB ZNF154
ZNF792 MHC2TA
WDR4 CD24
HUWE1 ARHGEF3
CD83 BIRC3
TRIB2 TRIM56
LARP1B HLA-DPB1
SLC38A5 UVRAG
AUH CD38
CTPS PEA15
CYTH1 FLJ10697
APOL3 TLR10
CHD6 ARHGAP10
IL1R1 HLA-DRA
LPCAT4 SHMT2
CITED2 LGALS9
DUSP4 FLJ10853
SSBP2 CEBPB
LAYN PRICKLE1
ZFAND2B LCP21
PIK3R1 CR1
GCNT4 KLHL14
PPP3CA TLR7
TIMP1 C20ORF72
SIRPG HLA-DQB2
CCR3 CORO1A
PTP4A3 PRKCE HECW2
SERINC5 FLJ25604
MAGOHB TRIM26
GIMAP4 FBXO41
KLHL24 GCNT1
CCNG2 LRMP
WDR70 UBE2J1
MYBL1 IGKV3D
CNPY4 PCCA
TIMM8A GLDC
CCDC28A CYSLTR1
MNAT1 BTLA
MS4A2 NET5
GZMB HLA-DPA1
E2F5 BLNK
HIBCH CD79B
C9ORF91 TM4SF8
NHP2 TFEB
CDC25B CD11ORF24
VDR ADRBK2
CSF1 CDKN2A
GPATCH4 RIPK2
NFKBID STX7
TMCO7 NCF4
EHBP1 SRGAP2
FAM173B SLC2A5
FARS2 CTSZ
FLVCR2 AIM2
NPM3 TCF4
PNPO TPD52
P2RY8 MAP3K8
TMEM63A MOBKL2B
MXI1 HLA-DOB
MRTO4 IFIT3
SESN2 MGC24039
C1ORF38 BRD4
STK38 RALGPS2
SLC6A6 SEMA4B
ALG14 BSG
LXN IGKC
TNFRSF18 HLA-DRB6
ACSS1 FUBP1
UBA7 UNC84B
MTSS1 IFNGR2
PSMA6 HSPA5
FAM8A1 HLA-DRB5
RAB31 MARCKS
TNRC6B KYNU
SESN1 PACAP
CEP68 RHOBTB2
LAPTM5 FLJ12363
PLAGL2 TMED8
LRRC33 FGD2
EIF2B3 FBXO10
URB2 IL4R
DDX21 CD1C
ITGA4 MGC50844
RGS2 MRPL49
RORC CTSH
IFNAR2 LYN
CSDA WASPIP
SORL1 C3ORF6
LRRC37B EGR1
IL10RA IGKV15
PRKACB SPAP1
CBWD1 CHERP
SMAD3 IGHG3
C1ORF96 ADAM28
FCER1A HLA-DMA
HSP90AB1 HLA-DMB
EMG1 PALM2-AKAP2
CD86
LAF4
LOC283663
FREB
DKFZP586A0522
UREB1
IGLL1
HLA-DQA2
KIAA1219
PLCG2
01-Mar
BCNP1
PNOC
CD20
PSCD1
BCL11A
VPS28
SWAP70
SYK
BCL7A
NAP1L
TEM6
BTK
RAB30
FCGR2B
STAT6
BRDG1
LOC201895
ITGB1
CD74
CORO2B
VPREB3
HSPC182
MGC15619
RHOH
IGHA
CYBASC3
KIAA0125
RAM2
CD83
FCRH1
FLII
SNX10
IGHG1
EPHX1
FLJ10979
GTPAP
IGLL3
E2F5
TNFRSF17
BLK
FLJ00332
SNX2
CD200
HLA-DQB1
TRIO
CYBB
PIK3AP1
IRF4
CD22
BACE2
IGJ
PAX5
RGS13
TCL1A
MEF2C
C13ORF18
POU2AF1
HHEX
IRF8
BANK1
OSBPL10
SLC2A1
NCF1
IGL@
IGLC2
SPAP1
IGHG3
HLA-DMA
HLA-DMB
CD79A
HSPA6
IGHD
KIAA0476
SLC7A7
NKG7
CD19
SAMD9
LY86
SPIB
NAPSB
RNASE6
IGHM
LY64
CD72
IRTA2
CD1D
HLA-DQA1
SAS
CTSH
LYN
WASPIP
C3ORF6
EGR1
FREB
DKFZP586A0522

dominikricken commented 4 years ago

Hi singscore team, Thank you for that great tool. I seem to face the very same problem as @hyojin0912 . I am interested in a expression signature, that involves upregulated genes only. Unfortunately, when executing generateNull() I get the very same error message as Hyojin did. Have you been able to solve that issue?

Thanks for your help!

Dominik

bhuvad commented 4 years ago

Hi @hyojin0912 and @dominikricken,

I apologise for the delay in attending to this matter. This was in fact a bug in the function which I have now fixed (15bbf84dcf73ca044fbaca909f34494a0a456a4f). Thank you for pointing it out to me and for your detailed reports. The update will be released as part of singscore (v1.8.0) in the next Bioconductor release (v3.11 end of Apr 2020). This update comes with a bunch of other bug fixes so I highly recommend updating it once its released.

Cheers, Dharmesh