Question: Filter transcripts based on expression value: TPM vs TMM ?
0
gravatar for Picasa
2.1 years ago by
Picasa470
Picasa470 wrote:

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.

tmm tpm transcriptome • 1.4k views
ADD COMMENTlink written 2.1 years ago by Picasa470
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 959 users visited in the last hour