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Pigengene
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Questions about using training sets and WGCNA module eigengenes generated separately for Pigengene package
Pigengene
6 months ago • updated 5 months ago
kjngo
▴ 40
2
votes
7
replies
966
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Errors with running learn.bn function and setting toCompact to TRUE in one.step.pigengene function in Pigengene package
Pigengene
6 months ago • updated 5 months ago
kjngo
▴ 40
6
votes
5
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1.4k
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Pigengene : BN network using consensus module
Pigengene
updated 5.5 years ago by
Habil Zare
▴ 200 • written 5.5 years ago by
rammohanshukla
▴ 10
3
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6
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1.4k
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Questions on Pigengene
Pigengene
WGCNA
updated 6.2 years ago by
Habil Zare
▴ 200 • written 6.2 years ago by
boting.m.ning
• 0
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Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Michael Love
42k
If you manually compute PCA on VST data, what are the top 5 genes contributing to PC1? https://github.com/thelovelab/DESeq2/blob/devel/R/p…
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Eric Katagirya
• 0
I created a DESeqDataSet object using DESeqDataSetFromMatrix function. I don't anticipate any mismatching or mixup of sampleIDs.
Answer: Assymetric MA plot with no overall trend
by
Michael Love
42k
> so many upregulated genes vs. downregulated, which I think is worrying Take a look at the plotCounts for a couple of the up-regulated …
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Michael Love
42k
I'm wondering about sample table mixup. How have you merged your sequencing data with the phenotype data (`colData`)?
Comment: Can I trust the differential expression analysis when the two groups overlap on
by
Eric Katagirya
• 0
Thanks @mikelove , Using vst or rlog doesn't improve the segregation nor is there a remarkable difference when I use 1000 or 2000 most vari…
Votes
Ensembl 112 has been released.
A: Diffbind results - non uniform width
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Answer: Error EPICv2 ChAMP
Comment: Store output of matchPWM()
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