Question: How to use TPM in plotMA in DESeq2
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3 months ago by
georgewwp0 wrote:

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$counts. Is this a good option? Is there a way I can access normalized TPM from within dds so that I can use the plotMA function? I discovered counts(dds) do not change after dds <- estimateSizeFactors(dds). How do I access the counts across samples after normalization? Thank you! George deseq2 tpm • 148 views ADD COMMENTlink modified 3 months ago by Michael Love21k • written 3 months ago by georgewwp0 Answer: How to use TPM in plotMA in DESeq2 2 3 months ago by Michael Love21k United States Michael Love21k wrote: You can use txi$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.