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Old 11-12-2013, 04:09 PM   #1
feralBiologist
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Default Differential Expression Using mixed libraries (truseq, nextera)?

I have 3 replicates for 2 conditions (6 samples) which have been sequenced using different protocols (nextera, truseq). Do I just need to use the library type as a blocking factor when defining the model for the differential expression?

I am planning to use edgeR but, I reckon, the same logic would apply to DESeq, too.
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Old 11-13-2013, 12:26 AM   #2
dpryan
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Yes, just use library type as a factor.
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Old 11-13-2013, 12:26 AM   #3
dpryan
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Also, cross-posted here.
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Old 11-13-2013, 04:56 PM   #4
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Quote:
Originally Posted by dpryan View Post
Yes, just use library type as a factor.
Thanks a lot!
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deseq, edger, nextera, rna-seq, truseq

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