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MonashProteomics / FragPipe-Analyst

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Filtering the proteinIDs and adjusted p-value calculation #82

Closed pejota66 closed 1 year ago

pejota66 commented 1 year ago

Hello,

Does the Fragpipe-Analyst perform the filtering of the data (i.e. remove contaminants, reverse and protein identified by site)?

What is the statistical method used behind to calculate the p-value which is further adjusted based on BH or local area based)?

Many thanks in advance

hsiaoyi0504 commented 1 year ago

@pejota66 Sorry for the late response. Yes, we remove contaminants, but I am kind of not sure what do you mean "reverse and protein identified by site"? Would you mind elaborating that? For statistical method, we used Limma as LFQ-Analyst.

hsiaoyi0504 commented 1 year ago

For more general filtering, those settings are in the advanced options.

hsiaoyi0504 commented 1 year ago

I am closing this since no further updates.

pejota66 commented 1 year ago

Sorry for my late response. If I am not mistaken "reverse and protein identified by site" is an option from Perseus software to filter/clean up the data.

Many thanks for your help.