Filter transcripts based on expression value: TPM vs TMM ?
0
0
Entering edit mode
4.6 years ago
Picasa ▴ 610

Hello,

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 abundance_estimates_to_matrix.pl) 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
ADD COMMENT

Login before adding your answer.

Traffic: 1529 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6