The Difference Between Rpkm And Raw Read Counts
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8.5 years ago
camelbbs ▴ 680

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 • 4.1k views
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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.

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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.

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What do you mean by "expression trend"?

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