Hi all,

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? 

Thank you!

George

You can use txi$abundance for the TPM measure. plotMA is a very simple function, you can probably most easily just write your own function that plots mean TPM on the x and log2FoldChange on the y, coloring points a different color if padj < threshold.