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

Hi CA,

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

Kind regards

Peter

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.