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Nesvilab / TMT-Integrator

A tool integrates channel abundances from multiple TMT samples and exports a general report for downstream analysis.
http://tmt-integrator.nesvilab.org
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[Question] tmt-integrator output #12

Closed skeffington closed 3 years ago

skeffington commented 3 years ago

Hi, I just want to be absolutely certain I'm not misinterpreting the tmt-integrator output:

1) The abundance based outputs (eg Report_abundance_groupby=protein_protNorm=None_gu=0.tsv) - are these still on a log2(intensity) scale?

2) I can't quite get my head around the Ratio based output: Are they the ratio to the reference intensity (this doesn't seem to fit when I compare to the Abundance table)? And are they also still on a log2 scale?

3) What aggregation method is used to get protein intensities from the chosen and normalised peptide intensities? Mean, geometric mean, median?

Sorry if I missed some of this in the docs - I just want to be sure!

Many thanks, Alastair

huiyinc commented 3 years ago

Hi Alastair

  1. Yes, both ratio- and abundance-based reports are in the log2 scale.
  2. Yes, the ratios are the channel intensity to the reference intensity (i.e., ratio=log2(the intensity of the ith channel/ the reference channel intensity).
  3. We use median for the aggregation.

Hope this helps. Thanks.

Huiyin

skeffington notifications@github.com 於 2020年12月4日 下午11:15 寫道：



Hi, I just want to be absolutely certain I'm not misinterpreting the tmt-integrator output:

1.

The abundance based outputs (eg Report_abundance_groupby=protein_protNorm=None_gu=0.tsv) - are these still on a log2(intensity) scale? 2.

I can't quite get my head around the Ratio based output: Are they the ratio to the reference intensity (this doesn't seem to fit when I compare to the Abundance table)? And are they also still on a log2 scale? 3.

What aggregation method is used to get protein intensities from the chosen and normalised peptide intensities? Mean, geometric mean, median?

Sorry if I missed some of this in the docs - I just want to be sure!

Many thanks, Alastair

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