I have cell lines where RNA was extracted and was split across two lanes giving me two technical replicates per sample. I have my read counts for each technical replicate and I am going to use edgeR to get a DEG list. Is there a program which will average the reads from the technical replicates? Thank you.
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Tota •
2 answers
so it's the same biological sample but just run on two different lanes (where the combinations is your requested #reads) ? If so, simply concatenate the two technical repeats into a single file and work with that one.
You don't have to do anything manually, if you tell edgeR which samples represent the same underlying biological sample in the design matrix, you should be set.
on top of what Friederike said, no, no need for averaging. That sample could just have well be run in a single lane, summing both will be enough (especially when each lane only contributes 1/2 of the amount of sequence you ordered)
edgeR povides the function sumTechReps() for this purpose.
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