how to calculate counts per million

[shirley47162928]

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

[GenoMax]

http://seqanswers.com/forums/showthread.php?t=40204

[Gordon Smyth]

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.

[diego diaz]

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

[Gordon Smyth]

# 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.

[diego diaz]

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.