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Vitek-Lab / MSstats

R package - MSstats
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Only partial results from dataProcess #80

Closed hanna6703 closed 2 years ago

hanna6703 commented 2 years ago

Hi,

I've been trying to analyse label-free DDA data using the MSstats.csv file from IonQuant. When using the dataProcess function, I've noticed that the resulting object is not a list of 5 but a list of 3. I contains FeatureLevelData, ProteinLevelData and SummaryMethod - with ProcessedData, RunlevelData, ModelQC and ProdictBySurvival missing (according to the manual "Protein significance analysis of mass spectrometry-based proteomics experiments with R and MSstats (v3.18.1) or later").

When using the inbuilt DDARawData the same happens, on my computer as well as on that of a friend. How can I obtain the processed data from dataProcess?

I'm using R 4.1.1, MSstats 4.2.0 and to get to the results I described I simply used dataProcess(DDARawData).

Thanks! Hanna

mstaniak commented 2 years ago

It's all OK, we will update the manual soon. Current package documentation described the latest version, so it's better to use that. dataProcess returns a list of 3.