Originally posted by GenoMax
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Unfortunately the rRNA depletion failed in about half of the samples and instead of re-doing the libraries the sequencing facility sequenced at a greater coverage instead...
They should have been run on the same machine and the only difference is that they were run at different times and then of course the contamination. However, if the rRNA contamination shouldn't cause any problems, I don't know why I can't control for this batch effect that I see in the PCA plot I have tried including batch in the model in DESeq2 and EdgeR. I have also tried correcting with RUVseq and ComBat. I am now looking into ImpulseDE2.
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