Question: The Difference Between Rpkm And Raw Read Counts
1
gravatar for camelbbs
7.8 years ago by
camelbbs680
China
camelbbs680 wrote:

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 • 3.9k views
ADD COMMENTlink modified 7.3 years ago by Biostar ♦♦ 20 • written 7.8 years ago by camelbbs680
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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 REPLYlink modified 7.8 years ago • written 7.8 years ago by Obi Griffith18k

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.

ADD REPLYlink modified 7.8 years ago • written 7.8 years ago by camelbbs680

What do you mean by "expression trend"?

ADD REPLYlink written 7.8 years ago by Steve Lianoglou5.1k
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