Open Rimanpreet1 opened 1 week ago
I subset one celltype from seuratobject and when I again integrated the subsetted object, it gave me error. i am using following code naive.split<- SplitObject(naive, split.by = "orig.ident") naive.split$HD1_Healthy
naive.merge<- merge(naive.split$HD1_Healthy, y=c(naive.split$HD2_Healthy, naive.split$P1_Convalescent, naive.split$P2_Convalescent, naive.split$P1_Acute, naive.split$P2_Acute))
naive.merge <- NormalizeData(naive.merge) naive.merge <- ScaleData(naive.merge)
naive.merge <- FindVariableFeatures(naive.merge, nfeatures = 2000)
when I run findvaribalefeature, it gave me this warning error "There were 23 warnings (use warnings() to see them)
warnings() Warning messages: 1: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : at -1.246 2: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : radius 0.00024168 3: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : all data on boundary of neighborhood. make span bigger 4: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : pseudoinverse used at -1.246 5: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : neighborhood radius 0.015546 6: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : reciprocal condition number 1 7: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : There are other near singularities as well. 0.031008 8: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : zero-width neighborhood. make span bigger 9: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : pseudoinverse used at -2.0354 10: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : neighborhood radius 0.30103 11: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : reciprocal condition number 1.4899e-14 12: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : pseudoinverse used at -1.7666 13: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : neighborhood radius 0.31947 14: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : reciprocal condition number 9.5274e-28 15: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : There are other near singularities as well. 0.090619 16: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : pseudoinverse used at -1.6986 17: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : neighborhood radius 0.3184 18: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : reciprocal condition number 3.894e-28 19: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : There are other near singularities as well. 0.031008 20: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : pseudoinverse used at -1.9226 21: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : neighborhood radius 0.49664 22: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : reciprocal condition number 1.5983e-14 23: In simpleLoess(y, x, w, span, degree = degree, parametric = parametric, ... : There are other near singularities as well. 0.090619"
and if I run PAC on same object, it got this " naive.merge <- RunPCA(naive.merge) Warning: The following 244 features requested have zero variance; running reduction without them: IGHV3-21, IGHV2-5, IGKV2-28, CRIP1, CD3E, IGKV1D-8, IGHV3-66, EGR1, CD9, IGKV1D-39, AC246787.2, IGHE, DUSP1, LCK, LINC01934, SELPLG, MT2A, SLC38A11, JUN, EEF1A1, C1orf162, RFX3, PCDH9, AUTS2, HIST1H4J, IFITM3, MPP6, SERPINA1, MAL, ITGB2, MYC, ALCAM, TMEM117, CCR7, IGHV4-28, IGHV3-53, DNAJB1, ACSM3, FAM118A, TIMP1, ANXA2, S100A6, GBP1, PDIA6, TMEM173, FGFBP2, TENT5A, SNTG2, RAD18, AC083837.1, IARS, ICOS, DRAM1, PRKCH, CCL3, MESD, FCN1, TMEM204, MRTFB, MARCKSL1, SUPT20H, CDC14A, AP3B1, GRK5, SLC25A28, ARL15, JAZF1, TSC22D2, NFATC3, IGKV1D-13, BAZ1B, HCK, EEF1E1, AC120193.1, BACH2, NEDD9, RABGEF1, ITK, PEAK1, CD44, WDR74, RASGEF1B, ASCC1, ELL, PELI2, RASA2, GNA12, RBL2, CREBBP, MICU3, KCNG1, NUP58, MPPE1, CASP4, MDP1, MTIF3, MYL6B, MAT2A, RPLP0, ANXA6, UBAC2, ARHGEF3, WASHC2C, LINC01473, ST8SIA4, LENG8, MARF1, ZMYND8, SLC12A6, MRPS25, DIAPH1, MARCH3, CHD2, CUX1, CLMN, SNRK, ATAD2B, APP, RAP1GAP2, ZC3H [... truncated] Warning in PrepDR5(object = object, features = features, layer = layer, : The following features were not available: MALAT1, FYB1, GIMAP4, HCST, XYLT1, B2M, KLF12, FLT3LG, FP236383.3, AMN, ABHD17A, CD99, MAP3K5, GIMAP7, OXNAD1, CLCN3, EEA1, SYTL3, IGF2R, ZAP70, IL10RA, STEAP1B, MRPL41, SPATA13, AOPEP, RAD51B, POU2F1, SMYD3, RNLS, GIMAP1, ZRANB3, DENND4A, RGS10, IL21R, PSMB4, ADGRE5, SGTB, ZNFX1, FOXN3, IGFLR1, SLC25A24, PRKN, ZFC3H1, PEBP1, ZFP36L2, VPS13A, DIRC3, ZNF10, ZDHHC20, FAM149B1, EMP3, B4GALT1, PHACTR4, RPS18, AGO4, HSPA4, ING1, TINF2, PSMA3, ARRDC2, SIK2, NUP88, FMNL1, LITAF, LIMS2, NR4A3, SCML4, HAUS3, C14orf28, MAP4K3, SERINC5, HOTAIRM1, VPS54, PLEKHB2, MYO1C, PLAAT4, CKLF, ACTN1, NEIL1, ADAM8, HIBADH, CC2D1B, LINC02256, NUBP2, ARMC1, LRRC8C, CLIP1, LCP2, MAP2K1, DENND4B, PITPNM2, LINC01128, KPNA2, RPS12, ZC3HAV1, GLIDR, DNAJC27, KIAA0930, HSPB1, USP6NL, ITGB2-AS1, HIST1H1E, RUFY3, RPA3, ZNF700, ZBTB10, AC008105.3, RC3H2, RNF213, GTF2H5, HCG17, MARCH5, NOC3L, LEPROTL1, SKAP1, RBM23, VCPIP1, MTRR, MANEA, CYTH1, GALNT11, IL10RB, NAA40, GTF3C4, DMX [... truncated]" i dont understand it, could you please me this?
I subset one celltype from seuratobject and when I again integrated the subsetted object, it gave me error. i am using following code naive.split<- SplitObject(naive, split.by = "orig.ident") naive.split$HD1_Healthy
naive.merge<- merge(naive.split$HD1_Healthy, y=c(naive.split$HD2_Healthy, naive.split$P1_Convalescent, naive.split$P2_Convalescent, naive.split$P1_Acute, naive.split$P2_Acute))
naive.merge <- NormalizeData(naive.merge) naive.merge <- ScaleData(naive.merge)
naive.merge <- FindVariableFeatures(naive.merge, nfeatures = 2000)
when I run findvaribalefeature, it gave me this warning error "There were 23 warnings (use warnings() to see them)
and if I run PAC on same object, it got this " naive.merge <- RunPCA(naive.merge) Warning: The following 244 features requested have zero variance; running reduction without them: IGHV3-21, IGHV2-5, IGKV2-28, CRIP1, CD3E, IGKV1D-8, IGHV3-66, EGR1, CD9, IGKV1D-39, AC246787.2, IGHE, DUSP1, LCK, LINC01934, SELPLG, MT2A, SLC38A11, JUN, EEF1A1, C1orf162, RFX3, PCDH9, AUTS2, HIST1H4J, IFITM3, MPP6, SERPINA1, MAL, ITGB2, MYC, ALCAM, TMEM117, CCR7, IGHV4-28, IGHV3-53, DNAJB1, ACSM3, FAM118A, TIMP1, ANXA2, S100A6, GBP1, PDIA6, TMEM173, FGFBP2, TENT5A, SNTG2, RAD18, AC083837.1, IARS, ICOS, DRAM1, PRKCH, CCL3, MESD, FCN1, TMEM204, MRTFB, MARCKSL1, SUPT20H, CDC14A, AP3B1, GRK5, SLC25A28, ARL15, JAZF1, TSC22D2, NFATC3, IGKV1D-13, BAZ1B, HCK, EEF1E1, AC120193.1, BACH2, NEDD9, RABGEF1, ITK, PEAK1, CD44, WDR74, RASGEF1B, ASCC1, ELL, PELI2, RASA2, GNA12, RBL2, CREBBP, MICU3, KCNG1, NUP58, MPPE1, CASP4, MDP1, MTIF3, MYL6B, MAT2A, RPLP0, ANXA6, UBAC2, ARHGEF3, WASHC2C, LINC01473, ST8SIA4, LENG8, MARF1, ZMYND8, SLC12A6, MRPS25, DIAPH1, MARCH3, CHD2, CUX1, CLMN, SNRK, ATAD2B, APP, RAP1GAP2, ZC3H [... truncated] Warning in PrepDR5(object = object, features = features, layer = layer, : The following features were not available: MALAT1, FYB1, GIMAP4, HCST, XYLT1, B2M, KLF12, FLT3LG, FP236383.3, AMN, ABHD17A, CD99, MAP3K5, GIMAP7, OXNAD1, CLCN3, EEA1, SYTL3, IGF2R, ZAP70, IL10RA, STEAP1B, MRPL41, SPATA13, AOPEP, RAD51B, POU2F1, SMYD3, RNLS, GIMAP1, ZRANB3, DENND4A, RGS10, IL21R, PSMB4, ADGRE5, SGTB, ZNFX1, FOXN3, IGFLR1, SLC25A24, PRKN, ZFC3H1, PEBP1, ZFP36L2, VPS13A, DIRC3, ZNF10, ZDHHC20, FAM149B1, EMP3, B4GALT1, PHACTR4, RPS18, AGO4, HSPA4, ING1, TINF2, PSMA3, ARRDC2, SIK2, NUP88, FMNL1, LITAF, LIMS2, NR4A3, SCML4, HAUS3, C14orf28, MAP4K3, SERINC5, HOTAIRM1, VPS54, PLEKHB2, MYO1C, PLAAT4, CKLF, ACTN1, NEIL1, ADAM8, HIBADH, CC2D1B, LINC02256, NUBP2, ARMC1, LRRC8C, CLIP1, LCP2, MAP2K1, DENND4B, PITPNM2, LINC01128, KPNA2, RPS12, ZC3HAV1, GLIDR, DNAJC27, KIAA0930, HSPB1, USP6NL, ITGB2-AS1, HIST1H1E, RUFY3, RPA3, ZNF700, ZBTB10, AC008105.3, RC3H2, RNF213, GTF2H5, HCG17, MARCH5, NOC3L, LEPROTL1, SKAP1, RBM23, VCPIP1, MTRR, MANEA, CYTH1, GALNT11, IL10RB, NAA40, GTF3C4, DMX [... truncated]" i dont understand it, could you please me this?