How can I use log2 RPM data(RNA-seq) to find differentially expressed genes?

Question

[Tommmm]

Hello everyone,I am a new guy to R and RNA-seq . And now I have a gene expression matrix ,but the type of it is not the "counts",but the "log2RPM" ,I have no idea how can I use it.The package "edgeR" and "DEseq2" doesn't seem to be able to receive this type of data ,they receive "counts" ,so what package shound I use? And what fuction shound I choose? Please help me!! Thank you all !

[ahmad mousavi]

Hi

For DEseq2 use this tutorial , See Count matrix input part.

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#count-matrix-input

[Ram]

Your comment does not mention that it doesn't address OP's principal question - the tutorial is for raw counts and does not mention RPM at all. You're giving OP information they already have while not addressing their question.

[Tommmm]

Oh!!! Thank you ,I'll read it carefully!!

Answer 1

[swbarnes2]

Limma might be able with counts like that, but the typical software, DESeq2 and EdgeR, will not. You should attempt to convert back to raw counts.

[Tommmm]

Thank you so much ,now I am tring to handle it with limma!