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hac141
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@hac141-11750
Last seen 6.7 years ago
I wonder if anyone has experience doing an analysis with 3 biological replicates for the treatment but only 2 for the control? I am almost certain I screwed up one of my control samples during the libraries construction and now PCA analysis shows that one of my control libraries clusters with the treatment libraries. Obviously DESEq is giving me basically no significant DE, while removal of the "bad" library gives me a result that makes sense.
Assuming your question is "is it OK to have different number of control / treatment replicates", then the answer is yes, it is OK.
Is the badly prepared control library the same as the one that plots with the treatments?
Could you provide more detail, such as the technique used (RNA-seq?) or the R script? That would help in answering.