How can I analyze normalized expression data?
I discovered a problem while trying to analyze RNA-seq expression data using DEseq2. DEseq2 is a tool for unnormalized data, that is, raw count, and my data is RPKM data. Since all I have is an expression matrix, I think it's difficult to convert it to a raw count. So, this is a headache. What tool should I use to find the different expression genes of normalized data such as RPKM or TPM?
1 answer
This has been issued a dozen times before. Have a look at Limma package.
https://support.bioconductor.org/p/126817/
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Bastien Hervé
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