I am getting the error message 'Q-value could not be calculated' for my most recent multigroup job in XCMS online. The peak picking and intensity values are all there, so I'm not sure what the problem is. I have run this job a few times with minor changes to the parameters, and for what it's worth the error seems to occur when I increase the prefilter intensity.
Should I be concerned that the q-values cannot be calculated? The overall peak picking looks good, and I'll be using a separate program for statistical analysis so I don't necessarily need to have the q-values calculated at this stage.
Stage,
This has happened because one or more than one of the p-values were not calculated and are NA's. This could be due to the all classes having the same intensity values and so the test could not be completed for that feature. For q-value calculation the p-value distribution is required. Missing values make the distribution uncertain and so q-values are therefore not calculated.
Cheers,
Paul