Deseq2 and co-expression network normalization
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lola • 0
@ebab691a
Last seen 9 weeks ago
Spain

Hi! So, I am doing a co-expression analysis on DEGs for a TCGA dataset.

I have used raw count data to find DEGs with DESeq2 and have around 300 of them. Now, I would like to proceed with co-expression analysis: should I normalize the raw count data I have or can I extract the DEGs from my original dataset (again, raw counts) and compute the correlation matrix between those? Or should I go back and download the FPKM data (which I know is normalized) and extract from that the DEGs I computed by providing the raw counts to DEseq2?

DESeq2 Normalization DifferentialExpression r • 207 views
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As you probably want a dedicated package for co-expression such as WGCNA...these have a FAQ that covers what sort of expression values to use and how to prefilter your data. Please read and follow it.

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@mikelove
Last seen 13 hours ago
United States

We usually use vst to look at gene-gene comparisons.