User: user56

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user5620
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Posts by user56

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IPA - gene list
... Hi, I did analysis in IPA (Ingenuity Pathway Analysis) on RNA-Seq data. I have my pathways but I would like to know what genes are present in particular Canonical Pathway. The ratio says for example 8/240 (8 genes from my dataset, 240 genes for the whole pathway). I am interested in these 240 genes ...
gene list ipa rna-seq canonical pathway written 9 weeks ago by user5620 • updated 9 weeks ago by genomax68k
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Comment: A: WGCNA for different comparisons
... Thank you very much for your help, that's exactly what I needed! ...
written 7 months ago by user5620
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Comment: C: RNA-Seq normalization using limma or DESeq2
... Thank you very much! I'm just thinking, because of the time it takes to run vst in WGCNA, if I could use both of them on different kinds of analysis (varianceStabilizingTransformation for PCA, up/downgenes heatmpas, fgsea and getVarianceStabilizedData for WGCNA). Why do you prefer rlog? What is th ...
written 7 months ago by user5620
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Comment: C: RNA-Seq normalization using limma or DESeq2
... Thank you. My data seems to be pretty noisy. Also, is it ok to use only DESeq2 without any other steps like vst? ...
written 8 months ago by user5620

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