I have read blogs on how to remove batch effects in deseq2 and how to visualize it using limma voom remove batch effect PCA. I'm not sure if the batch effect was removed in my analysis. Please find the attached output, I'm skeptical because in heat map they seem to cluster separately (with respect to batches).
Analysis: 51 samples with two batches (Batch1 includes NYGC in the label and Batch2 doesn't include NYGC in the label). The two batches are rnaseq data from different sequencers.
PCA before removing batch effect
PCA after removing batch effect
Heat map with batch factor included in design formula
design =~ Gender+ageRange+Batch+Cond
Heat map without batch factor in design formula
design =~ Gender+ageRange+Cond
I'd be really great if anyone could validate my results. Thank you!