Need help in doing proteomics analysis
Hello everyone. Greetings of the day.
I need help in doing proteomics analysis.
I have MaxQuant output files that contain files :
aifMsms.txt, allPeptides.txt, evidence.txt, modificationSpecificPeptides.txt, msms.txt, msmsScans.txt, msScans.txt, mzRange.txt, Oxidation (M)Sites.txt, parameters.txt, peptides.txt, proteinGroups.txt, simPeptides.txt, simScans.txt, summary.txt .
I don't understand how to further perform differential expression analysis in R through these files.
I am new to proteomics analysis. So, any help would be appreciated.
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cpad0112
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rishav513 •
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rishav513 •
2 answers
Bioconductor has several packages starting from MaxQuant with extensive manuals that guide your through the DE endeavour, e.g.:
https://bioconductor.org/packages/release/bioc/vignettes/DEP/inst/doc/DEP.html
you can also consider galaxy for the same. Here are tutorials:
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