Closed tobiasko closed 2 years ago
The abundances from Philosopher output files are all "raw". The idea is to provide people with the raw values so they can followup with their preferred post-processing tools and methods. You can use TMT-Integrator to filter, clean, and normalize your abundances, in a way that you can easily use them to make any assumptions. Our go-to method is based on TMT-Integrator, which uses reference channels to normalize the abundances. It's a common practice to use pooled channels when you have multiple experiments in different plexes, like you do. If a pooled (a.k.a. bridge) channel is missing, TMT-I can also generate what we call a virtual channel to use as a reference and calculate the ratios. As an option, the program can also revert the ratio calculation and print straight abundances.
Great! That helps a lot. THX!
I am trying to analyse 2D-TPP data (5x TMT10plex in fractions) using the bioconductor package TPP2D. The package expects the input data (protein level abundance estimates) as tabular data per TMTnplex sub experiment presented as list. I generate such a data structure by reading in the
protein.tsv
files found in the experiment folders (here named: T1_2, T3_4, ...). Here is a listing of the FragPipe output folder:My
protein.tsv
file look like this:My question: Are the protein abundance estimates reported in
protein.tsv
(columns A1, B1, C1, ...) the raw reporter ion intensities? Or are they already transformed in some way? The TMTintegrator settings only affect the output written to thetmt-report
folder?Your webpage says
additional columns for TMT/iTRAQ channels if applicable, each contains relative reporter ion abundances
Really relative, not abs.? Relative to what?
logs are attached log_2022-06-27_14-34-00.txt