Corey Broeckling

I have long been removing exceptionally wide chromatographic peaks after feature detection but before correspondance. Old XCMS data structure: if(filtPeaks) { orig

@jorainer - thanks. i didn't try removing smoothing and will give that a go. I guess i was just puzzled why i couldn't find any settings that worked without an...

warnings seems like a perfectly acceptable option. Re. old xcmsSet - guilty as charged in this area. I am using new for some workflows, but this isn't yet a large...

Thanks you @jorainer. I will adapt the old code to new. I was trying to find the source of the error message yesterday too and it does seem pretty well...

troubleshooting: ``` ### XCMS feature detection cwp

Of course - https://drive.google.com/open?id=1OBW7XOXWb3r8K2cOyDDoIy7Ksee43vzX There are four files present. Each is a different sample, converted from waters MSe .RAW to mzML using proteowizard. The data is centroided at acquisition. I...

Thank you! I will try this ASAP. Re. what to do next, nothing in XCMS, I hope. At this point we have an XCMS object that is used as input...

@jorainer : Follow up question: I noticed that sampleGroups argument in the PeakDensityParam() function requires a vector the same length of the number of files (4, in my test set),...

Thanks for the detailed response. I guess I failed to clearly present the workflow I have been using for the past several years in the old format. As I had...

I have implemented a functional 'trick XCMS' method, in reference on option 2 above. - export MS1 data and MSe (MSMS) data as two separate files - the list of...