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  • 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.

  • #2
    Yes, just use library type as a factor.

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    • #3
      Also, cross-posted here.

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      • #4
        Originally posted by dpryan View Post
        Yes, just use library type as a factor.
        Thanks a lot!

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