How can I use log2 RPM data(RNA-seq) to find differentially expressed genes?
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5 weeks ago
Tommmm • 0

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 !

log2RPM RNA-seq • 323 views
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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.

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

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4 weeks ago

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.

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

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