Hello,
I am using the LCMS preprocessing workflow and am having problems with groupChromPeaks. I have a dataset with samples, blanks and pools as classes (second column of metadata). Running groupChromPeaks using these classes and parameters below works well:
Method to use for grouping: PeakDensity
Bandwidth: 5.0
Minimum fraction of samples: 0.3
Minimum number of samples: 32 (blank+1)
Width of overlapping m/z slices: 0.001
Maximum number of groups to identify in a single m/z slice: 100
Reported intensity values: into
I wanted to use different classes. This time I used the treatment column as the class (2 treatments in total). I ran into the error:
Fatal error: Exit code 1 ()
Processing 157986 mz slices ... Error in if (!any(tt/sampleGroupTable[names(tt)] >= minFraction & tt >= :
missing value where TRUE/FALSE needed
Calls: groupChromPeaks ... .local -> do_groupChromPeaks_density -> .group_peaks_density
Execution halted
Initially, I used these parameters:
Method to use for grouping: PeakDensity
Bandwidth: 5.0
Minimum fraction of samples: 0.5
Minimum number of samples: 8
Width of overlapping m/z slices: 0.01
Maximum number of groups to identify in a single m/z slice: 100
Reported intensity values: into
I have tried playing with these parameters a bit (increasing and decreasing bw and minFraction) but I still get the same error. For minimum number of samples, I put the number of samples of the class that has the lower number of samples.
Do you have any suggestion on what else I can try?
Clarification: For the pool and blank samples, I left the sampleClass empty, could this be causing the problem?
Thank you,
Rina
