Hi, I think this questioned has been asked before in different ways, but maybe someone can help mw understand this a bit better. My question stems from the need to visually represent the expression levels of a gene between my two groups. I know plotCounts() uses the normalized counts from counts(dds, normalized=T), but when I look at the total read counts per library, I realized that the DESeq2 normalization didn't quite resulted in equal count sizes between my libraries(samples). Is this expected, or is there a parameter I am mising to have equal reads across libraries? Along this line, if I want to visually represent the expression changes of a gene, should I be using the normalized counts from counts(x, normalized=T) as the plotCounts() does, or should I be using the counts from rlog() or vst()? Thank you for your help. My counts are below.
colSums(counts(dds)) WT_rep3 WT_rep4 WT_rep13 WT_rep14 Null_rep1 Null_rep2 Null_rep3 Null_rep4 25372528 25524255 35306510 34688537 28857148 29386607 28380245 24795934 Null_rep11 Null_rep12 66139067 34391514 colSums(counts(dds, normalized=T)) WT_rep3 WT_rep4 WT_rep13 WT_rep14 Null_rep1 Null_rep2 Null_rep3 Null_rep4 32400476 31980209 30906366 31123613 32129757 32307761 32902001 31931771 Null_rep11 Null_rep12 31123321 3126603