How can I use log2 RPM data(RNA-seq) to find differentially expressed genes?
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 !
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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
Oh!!! Thank you ,I'll read it carefully!!
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.