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Question: How to normalized SWATH proteomic data?
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gravatar for carandres74
21 months ago by
carandres740 wrote:

Hello

I´m trying to normalize proteomic SWATH data from a proteomic analysis of CSF. I´ve try the DESeq2 package without success. Could any one recommend a specific R package or way to do this?

Kind regards,

CA

ADD COMMENTlink modified 21 months ago by Laurent Gatto840 • written 21 months ago by carandres740
0
gravatar for blattmann
21 months ago by
blattmann0
Switzerland/Zurich/ETH Zurich
blattmann0 wrote:

Hi CA,

you can use the R package MSstats or the tool mapDIA (http://sourceforge.net/projects/mapdia/).

Kind regards

Peter

ADD COMMENTlink written 21 months ago by blattmann0
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gravatar for Laurent Gatto
21 months ago by
Laurent Gatto840
United Kingdom
Laurent Gatto840 wrote:

You are the only one that can answer your question at this stage. What is needed is not a function/package that normalises label-free MS data, but there is a need to explore the data and assess what is to be expected/required by normalising it. And, once a data processing has been applied, to verify that the data was transformed adequately.

ADD COMMENTlink written 21 months ago by Laurent Gatto840
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