Is it possible to convert "DESeq2's normalized counts" to "DEGs"?

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Abhijeet Singh

Did you check/read the manual?

Wei Zhou

Of course! As the help documentary file of DESeq2 R package described, you could input the counts into the readin function of DESeq2 at the first step. In other words, you could restart the DESeq2 analysis.

Hicham Hboub

Abhijeet Singh Yes I have checked manual and vignettes of DESeq2, but they didn't mentionne the possiblity of this conversion.

Wei Zhou What's the pipeline to restart DESeq2 analysis from a preanalysed data ? I didn't found anything about it.

with raw data yes it's possible.

Hi, Hicham Hboub.

Sorry for my late reply. I mean if your data is still counts, you can actually analyze your data following the regular DESeq2 pipeline. Otherwise, if your "normalized counts" data is FPKM or TPM table, I think you shouldn't try to analyze it by DESeq2 suites. Because this pakage doesn't recommend any normalized data except counts. However, I suggest you to try limma or edgeR packages for further analysis of differentially expressed genes (DEGs). If you have any other questions about limma or edgeR usage, you could send a message to me at [email protected].

Good luck!