RSEM to CPM?

Hello,

I download the bulk RNA data from the cbioportal. The count is RSEM. I want to convert RSEM into CPM. Anyone know how to do this!!! Thank you for your help!!!

rna rna

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updated 5.4 years ago by ATpoint

• written 5.4 years ago by hq.huang11.6 •

1 answer

You can read RSEM output into tximport to summarize it to the gene level (tximport) and then feed it to any tool th get normalized counts, e.g. DESeq2 or edgeR:

http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html

http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#DESeq2

http://bioconductor.org/packages/release/bioc/vignettes/tximport/inst/doc/tximport.html#edgeR

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written 5.4 years ago by ATpoint

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