Filter transcripts based on expression value: TPM vs TMM ?
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4.6 years ago
Picasa ▴ 610


I have a transcriptome that I would like to filter by expression value. Basically, I have 3 samples that I mapped against my transcriptome with kallisto.

I have then use Trinity tool to produce an expression matrix, which gave me 2 matrix:

  • a matrix of TPM expression values (not cross-sample normalized): 1st matrix
  • a matrix of TMM-normalized expression values (or TMM-normalized TPM matrix): 2nd matrix

My first idea was to keep transcript (so contig) that have >=1 TPM in at least one sample (so using the 1st matrix).

Now I have doubt, should I use the TMM one instead ?? because results are a bit different.

Indeed, with the TPM values (1st matrix) I keep 30% of my initial transcriptome, while with the TMM values (2nd matrix) I keep 23% of my initial transcriptome

Thanks for your help.

transcriptome tpm tmm • 2.3k views

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