I'm running an RNA-Seq analysis for which I have 72 samples (mice), (6 replicates for each observed group). The main covariates are sex (MvsF) and cell type (A, B, C) from different tissues. Using voomWithQualityWeights() instead of voom() returns a lot more diferentially expressed genes (2-3 folds more). I was wondering how can I know for sure if I should use voomWithQualityWeights() or not?
I understand it has to do with sample heterogeneity and outliers. How can I know if my samples truly are heterogeneous and whether my outliers are significant enough to justify using voomWithQualityWeights() instead of regular voom()? I only have on 1-2 samples that seem to be acting as outliers on the MDS plots. But as I have 72 samples I think it should be ok to simply remove them and run the analysis with regular voom(). Is there any way to better test or know which voom method I should use?
Already asked on Biostars, where I linked to answers on Bioconductor: https://www.biostars.org/p/424507/#425165