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smorabit / hdWGCNA

High dimensional weighted gene co-expression network analysis
https://smorabit.github.io/hdWGCNA/
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Warning when using ModuleEigengenes #200

Closed yizhang-zoey closed 3 months ago

yizhang-zoey commented 4 months ago

When I run:

seurat_obj<- ScaleData(seurat_obj, features=VariableFeatures(seurat_obj))
seurat_obj<- ModuleEigengenes(
    seurat_obj,
    wgcna_name = 'celltype1',
)

I got the following warning message:

Centering and scaling data matrix
[1] "royalblue"
Centering and scaling data matrix

Warning message in irlba(A = t(x = object), nv = npcs, ...):
“You're computing too large a percentage of total singular values, use a standard svd instead.”
Warning message:
“Keys should be one or more alphanumeric characters followed by an underscore, setting key from pcaroyalblue to pcaroyalblue_”
Warning message:
“Requested number is larger than the number of available items (50). Setting to 50.”
Warning message:
“Requested number is larger than the number of available items (50). Setting to 50.”
Warning message:
“Requested number is larger than the number of available items (50). Setting to 50.”
Warning message:
“Requested number is larger than the number of available items (50). Setting to 50.”
Warning message:
“Requested number is larger than the number of available items (50). Setting to 50.”
pcaroyalblue_ 1 
Positive:  ERMP1, IPO9, COPRS, PPP1R9A, ICA1, PEX7, ARHGEF39, HOXB3, MACROD1, RPH3AL 
       KYNU, CCR2, MAPK12, KIF5C, PINLYP, TRIM16L, VGF, STPG1, DACT3, GLIPR1L2 
       TRIM2, FLRT2, LDHD, FCRL1, C12orf60 
Negative:  MYO16, PTGES, KLHL41, IGDCC4, IL13RA2, CA3, CCDC148, SLC45A3, CFI, CD101 
       NR2F1, KCNN2, STARD13, MLXIPL, DOCK6, FHDC1, TMEM45B, CAND2, COBL, LRP6 
       IGSF3, MAGI1, OCLN, VWCE, ARHGEF10L 
pcaroyalblue_ 2 
Positive:  IPO9, RPH3AL, HOXB3, KYNU, PEX7, DACT3, PINLYP, ARHGEF39, TMEM45B, DOCK6 
       MLXIPL, KLHL41, CAND2, CA3, PTGES, CD101, FCRL1, MYO16, IGDCC4, CCDC148 
       SLC45A3, VWCE, IL13RA2, FLRT2, COBL 
Negative:  COPRS, ERMP1, PPP1R9A, ICA1, MACROD1, CCR2, KIF5C, OCLN, TRIM16L, MAPK12 
       LDHD, TRIM2, C12orf60, FHDC1, GLIPR1L2, MAGI1, NR2F1, CFI, VGF, ARHGEF10L 
       LRP6, IGSF3, STPG1, STARD13, KCNN2 
pcaroyalblue_ 3 
Positive:  ERMP1, PPP1R9A, OCLN, CCR2, GLIPR1L2, COBL, FHDC1, STARD13, KCNN2, PTGES 
       VWCE, TMEM45B, IGDCC4, DOCK6, MYO16, MLXIPL, KLHL41, CFI, IL13RA2, DACT3 
       MAPK12, CCDC148, SLC45A3, PINLYP, STPG1 
Negative:  COPRS, IPO9, PEX7, ARHGEF39, ICA1, MACROD1, KIF5C, C12orf60, RPH3AL, TRIM2 
       TRIM16L, HOXB3, MAGI1, KYNU, CD101, FCRL1, LRP6, FLRT2, IGSF3, CAND2 
       LDHD, VGF, CA3, ARHGEF10L, NR2F1 
pcaroyalblue_ 4 
Positive:  PPP1R9A, PEX7, ICA1, IPO9, RPH3AL, MACROD1, HOXB3, CCR2, ARHGEF39, KIF5C 
       VGF, KYNU, PINLYP, GLIPR1L2, C12orf60, TRIM2, MAPK12, LDHD, TRIM16L, DACT3 
       LRP6, ARHGEF10L, DOCK6, CFI, FCRL1 
Negative:  ERMP1, COPRS, OCLN, STPG1, CD101, KCNN2, FLRT2, NR2F1, COBL, KLHL41 
       SLC45A3, MYO16, STARD13, PTGES, CCDC148, IL13RA2, CA3, CAND2, IGSF3, IGDCC4 
       MAGI1, TMEM45B, FHDC1, VWCE, MLXIPL 
pcaroyalblue_ 5 
Positive:  PPP1R9A, IPO9, ICA1, CCR2, STPG1, KIF5C, VGF, VWCE, C12orf60, TRIM16L 
       TMEM45B, GLIPR1L2, DACT3, FLRT2, CFI, IGSF3, CAND2, STARD13, MAGI1, LRP6 
       TRIM2, COBL, MYO16, ARHGEF10L, KLHL41 
Negative:  PEX7, ERMP1, COPRS, MACROD1, RPH3AL, HOXB3, ARHGEF39, KYNU, FCRL1, OCLN 
       MAPK12, LDHD, CD101, CA3, PINLYP, MLXIPL, DOCK6, PTGES, IGDCC4, CCDC148 
       NR2F1, FHDC1, KCNN2, IL13RA2, SLC45A3

Could I ignore the above warning message?

smorabit commented 3 months ago

No need to worry about these warning messages, you can just ignore.