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  • how to calculate counts per million

    Hi all,
    Could anyone tell how to calculate counts per million (CPM) manually? How it was calculated in edgeR related to RNA-seq data?

  • #2
    Discussion of next-gen sequencing related bioinformatics: resources, algorithms, open source efforts, etc

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    • #3
      Which edgeR CPM do you mean in particular? Do you mean the column called logCPM in the topTags table? That is computed using the aveLogCPM() function.

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      • #4
        To calculate CPM manually in R it would be :

        cpm <- apply(countmatrix,2, function(x) (x/sum(x))*1000000)

        # the 1 added to log function is to avoid log 0 values
        log.cpm <- log(cpm + 1)

        To calculate rpkm you have to know the gene lengths

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        • #5
          Originally posted by diego diaz View Post
          # the 1 added to log function is to avoid log 0 values
          log.cpm <- log(cpm + 1)
          That is not quite the same as what edgeR's cpm() function does. It's somewhat better to offset the counts rather than the cpms.

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          • #6
            Originally posted by Gordon Smyth View Post
            That is not quite the same as what edgeR's cpm() function does. It's somewhat better to offset the counts rather than the cpms.
            Yes, sorry, my mistake. The offset is added to the counts, not to the cpm.

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