How to normalized SWATH proteomic data?
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@carandres74-9625
Last seen 6.6 years ago

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

proteomics SWATH • 1.3k views
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Peter • 0
@peter-8503
Last seen 21 months ago
Switzerland/Allschwil/Idorsia

Hi CA,

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

Kind regards

Peter

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@laurent-gatto-5645
Last seen 13 hours ago
Belgium

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.

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