Hi,
Just to note, I posted a similar problem recently:
Repeated uniprot accesions and weird qvalues of proteomic data in the analysis tool
It doesn’t show in the screencap but I’m guessing that numCellLines was variable across compounds. In my case (running pearson correlation for MetMap500 vs Proteomic data) it seemed that when values were present across all queried cell lines (numCellLines=all cell lines queried), the pvalue was adjusted (in some way that I haven’t been able to replicate though), but for the rest of the cell lines it’s often just pvalue=qvalue.
I think there’s is a problem with the pvalue adjustment when some of the queried cell lines have no values…
