Yeah, bioinformatics can be quite frustrating... Although, the feeling is great when you get it done and you see all those beautiful tables with genes, aligned with p values and so on 
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Hey guys, is there an extra step needed for DESeq to adjust for library size?
What I mean is, I have three replicates, and two of them have half as many reads as the first.
So my file after pasting it into Excel, looks like this
Untreated Treated
Gene 1 6 3 3 8 4 4
Gene 2 10 5 5 12 6 6
.....
I then use this table to use for DESeq. Does DESeq adjust for each sequencing depth?Comment
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This is covered in the DESeq vignette, see also the "estimateSizeFactors" command, which is part of the standard work flow.Originally posted by billstevens View PostComment
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yeah sorry, I was just about to write that.Comment
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