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Old 08-29-2011, 07:43 AM   #4
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 994

I also realized after posting that the thread I mention talks about SNPs, not gene expression, but the problems are similar.

50bp single-end is definitely sufficient to get good expression values.

I don't know that much about cancer transcriptomics, but 10 samples sounds like a quite small number to me, especially without matched normal tissue, unless the expression differences between your sub-types are quite pronounced. Better have a good look at the literature (also look at microarray studies, the power issues should be quite similar) to see what sample sizes gave good results in the past.
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