I'm doing RNAseq analysis with DESeq2. When making MA plot, I want to position each gene on the x-axis using its mean abundance from one condition instead of rowmeans from counts(dds) across samples. This way, x-axis would carry information I'm interested in.
I quantified the transcripts using salmon and summarized at the gene level using tximport.
I'm thinking I could do
txi <- tximport(files, type = "salmon", tx2gene = tx2gene, countsFromAbundance = "lengthScaledTPM") and use txi$counts. Is this a good option?
Is there a way I can access normalized TPM from within dds so that I can use the plotMA function?
I discovered counts(dds) do not change after dds <- estimateSizeFactors(dds). How do I access the counts across samples after normalization?