Dear Julie
Thank you for your question. It would however be more appropriate for
the support forum, not for the developer mailing list. Would you mind
moving it there, perhaps also the responses so far?
There is no "in-principle" reason why DESeq2 shouldn't produce useful
results also for count data from technologies that are not
DNA-sequencing based. It's error model (Gamma-Poisson, GP) is quite generic.
As always, you should do model fit diagnostics though, to see whether
the residuals for each protein across replicates and conditions (after
fitting the GLM) are reasonably consistent with the GP, in particular,
that they look unimodal.
One issue to check is also whether the normalization (size factors) is
appropriate.
There is another bit of irony afaIu: If you have enough replicates (or:
degrees of freedom) that you can actually "see" deviations from the GP
assumption (i.e. >=dozens), then you probably don't need a parametric
method, and could switch to something non-parametric.
Kind regards
Wolfgang
6.1.18 18:45, Cardin Julie via Bioc-devel scripsit:
Hi,
I have experienced very good results with DESeq2 for my RNASeq analysis. As
far as I understand, it is a tool that normalise our data from sequencing to
make them comparable.
I have a new project implicating proteins counts.
I have couple of data sets. For each sample we have:
rows with proteins names (instead of genes), with their respective counts.
My goal is again to make a differential expression between treated groups
versus controls.
I wonder if I can use DESeq2 to do a differential expression for proteins?
Or if the correcting factor that is used by DESeq2 to correct counts for RNASeq
is specific to DNA sequencing and it is not applicable to proteins?
Is there a tool that do the exact same thing as DESeq2 but for proteins?
Thank you very much for your help and time,
Best regards and happy new year!
Julie Cardin
Bioinforamatician
IRCM
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With thanks in advance-
Wolfgang
-------
Wolfgang Huber
Principal Investigator, EMBL Senior Scientist
European Molecular Biology Laboratory (EMBL)
Heidelberg, Germany
wolfgang.hu...@embl.de
http://www.huber.embl.de
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