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.
I am planning to use edgeR but, I reckon, the same logic would apply to DESeq, too.
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