I'm trying to analyze some RNAseq results, but one of my samples is a pretty bad outlier by PCA and by clustering over the entire transcriptome.
I have 4 groups with 3 biological replicates. These samples were run in 2 batches.
When I try to summarize my reads using RSubread's featureCounts, the outlier has a very low assignment %, with a high % of multiple assignments
My question is how should I proceed with my analysis? I don't have enough replicates to kick the outlier out. Are there methods to fix outliers? Is it valid to consider this outlier as a separate batch (Removing the variation with removeBatchEffect)?