Which package is appropriate to the normalised RNA-seq data for differential expression analysis?

Question

[b.lin]

Dear all,

I am new for RNA-seq analysis. I have normalized data rather than raw count for RNA-seq, and i want do the differential expression study (negative binomial model). Is anyone can recommend one R package to handle this kind of data? As I study from DESeq, it is only accept raw count data. Any answer is appreciated!

[VHahaut]

I think you will have to be more precise about the normalization applied to the data (and maybe where are they coming from). It would be easier for us to help you.

Answer 1

[John Ma]

If the reads are already in FPKM or TPM, you can log-transform it and then perform linear regression with limma. The major negative-binomial packages (DESeq2 and edgeR) don't accept normalized reads.