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Old 01-10-2013, 05:50 AM   #5
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

Have a look at the "Filtering by overall count" section of the DESeq vignette, which I'll just copy and modify below:
rs = rowSums(counts(cdsFull))
use = (rs > 20)
cdsFilt = cdsFull[use,]
The actual threshold that's best will probably vary by sample number, it's convenient to make the plot they have in the vignette as "Figure 9" so you can eyeball if the threshold is inappropriate. See also "Figure 10".
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