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Forum: Bioinformatics 01-28-2013, 05:40 PM
Replies: 4
Views: 2,057
Posted By danielfortin86
EdgeR cpm values after batch effects

Is there a way to obtain the CPM values from EdgeR after batch correction? The "cpm" function only returns values after library size normalization. When I look at the result of glmFit there are...
Forum: Bioinformatics 10-05-2012, 04:56 PM
Replies: 7
Views: 7,440
Posted By danielfortin86
Thanks! I was interpreting the documentation as...

Thanks! I was interpreting the documentation as meaning that the average was calculated for specific factor level combinations / contrasts. Wouldn't plotting the actual "A" for a specific contrast be...
Forum: Bioinformatics 09-28-2012, 12:57 PM
Replies: 7
Views: 7,440
Posted By danielfortin86
EdgeR LogCPM Bug?

When I output the logCPM values for my genes, they are identical across contrasts. However, when I output the logFold values these seem to be correctly calculated for each contrast. Is this a bug or...
Forum: Bioinformatics 04-07-2010, 02:56 PM
Replies: 10
Views: 5,185
Posted By danielfortin86
I'm also having the same problem. What was the...

I'm also having the same problem. What was the solution?
Forum: Illumina/Solexa 02-06-2009, 04:02 PM
Replies: 145
Views: 286,466
Posted By danielfortin86
Adapter sequence

i know that the overhanging T is used to ligate with the added A from the DNA library, but thy is there a one base pair overhang on the other side? If you see how the sequence anneal there is an...
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