Fragpipe analyst giving multiples of identical p-values

Nesvilab / FragPipe-Analyst

An easy-to-use and interactive web application for FragPipe

https://fragpipe-analyst-doc.nesvilab.org/

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Fragpipe analyst giving multiples of identical p-values #23

Closed TBDerm closed 5 months ago

TBDerm commented 6 months ago

Hi all, I have recently uploaded a DIA intensity proteins dataset to fragpipe analyst, to get fold change and p-values. Contrary to other datasets I have analysed previously, this one is producing multiple identical p-values, so that when I make a volcano plot, there are several plateaus of points. Could anyone provide an explanation for this? Volcano plot is attached. Thanks!

hsiaoyi0504 commented 5 months ago

Thanks for the feedback. @TBDerm It's possible to have adjusted p-value or p-value the same. It's really typically when you have a comparison not really seeing difference like this case. I don't think that's really an issue of the program. Thanks.