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Old 10-11-2008, 08:07 AM   #7
Location: US

Join Date: Feb 2008
Posts: 13
Default normalization

Hi Chema,
Yeah I see what you mean. I guess most of the conditions we ran so far do not have the a huge amount of genes downregulated in comparison with the rest of the genes studied. We are doing whole genome RNA-seq studies and I think the house keeping genes do help avoid this problem.

In case having a huge number of genes that are indeed different, then maybe we have to come up with a slight modification of the RPKM formula/method to cope with this elevated expression or lack of. Maybe include a coverage based on the estimated level of expression variable.

Does anybody else used the RPKM method? Can you share with us the different normalization methods you might use for doing RNA-seq outside of RPKM?

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