R package for differentially expressed genes on cpm normalized data
Hi. I want to find differentially expressed genes in my RNA-seq data, but don't know which package is appropriate. I can not use DEseq2 because my data are CPM(count per million) normalized and log1p (natural log) transformed. while DEseq2 need row count data. Any useful suggestions would be appreciated.
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Hello, I am sorry to close this but this has been asked many times before and you do not seem to have invested any effort in finding or reading these posts. I will link one of many questions (here from the Bioconductor support forum) where the edgeR senior author answered this question. He recommends using the normalized data on the log scale and feeding them into limma-trend. If there are specific questions after reading the available matial both via our search function and google feel free to comment, we might reopen the question. You can also comment on existing threads which is probably preferable to keep information focused.
https://support.bioconductor.org/p/92303/