The Difference Between Rpkm And Raw Read Counts

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11.2 years ago

camelbbs ▴ 710

Hi All,

I have a question about raw read counts and rpkm. After I get gene counts and fpkm from cufflinks, I found some housekeeping genes (ACTB, GAPDH, RPLP0, UBC) have the similar expression trends in counts and rpkm.

I don't understand why. Does that mean the normalization in rpkm have no affections to housekeeping genes?

Thanks a lot! Cam

rnaseq • 5.0k views

ADD COMMENT • link updated 10.7 years ago by Biostar 20 • written 11.2 years ago by camelbbs ▴ 710

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Are the genes of similar size and your libraries of similar depth? If so, then they should have very similar trends as you will be essentially dividing by common factors. Of course, this will not always be the case, but it is not necessarily cause for concern.

ADD REPLY • link 11.2 years ago by Obi Griffith 20k

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Thanks. I think that may be caused by normalization with the total read counts(~N millions) in one sample, not with the gene read counts in all mRNAs. The total read counts are too big, so we get similar size factors.