an important question upfront is unfortunately still, whether the computers in the Lab are windows or Unix/Linux. I doubt that the efforts to get distributed jobs on windows to run reliably will be worth it.
But a beefy PC should be able to do it just fine, look for e.g. Intel 6core and at least 12GB RAM (or 16GB), they should sell between €1000,- (no-name) and €2000 (brands like HP or Fujitsu). With such a machine you can use nSlaves=6 or even =12 (Hyperthreading), and it should be able to finish 70 samples over lunchtime or an extended coffee. YMMV.
in the case of custom locations for netcdf you will have to unpack the mzR sources and edit mzR/src/Makevars to add your locations to PKG_CPPFLAGS and PKG_LIBS.
...But I am not able to read it into any other programme such as ADMIS ("Cannot read header record in GC/MS data file"), ChemStation (... is not a compatible AIA file)"
I have extended the CDF export in xcms, could you try http://msbi.ipb-halle.de/~sneumann/ko16-xcms.cdf and report if that works ? It loads in AMDIS without error, but doesn't look great. Can you check other programs ?
If you have y friendly bioinformatics or IT staff around, you could suggest to set up a real (or virtual) Linux machine somewhere, and check out the Rstudio server (http://www.rstudio.org/docs/)
Typically, such a real or virtual Linux machine would be closer to the central file storage compared to a normal windows machine in the office, which also helps file read/write performance.
this is great, and I am more than happy to help you as best as I can. So for MRM we'd first need to find out how to read the raw data into xcmsRaw, and then verify that centWave (or matchedFilter) can process it.
1) What format does MRM data come in ? Of course mzData/mzXML/mzML are preferred. Can we haven an example ?
2) I am happy to put a few trimmed down raw files into the msdata package, so that you can create manpages and a vignette around it.
Yours, Steffen
P.S.: Depending on your preferences, we can also take the discussion to the xcms-devel list. As you wish.
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How did you put the UV data into th excmsRaw ? As one "spectrum", where each RT datapoint becomes a "m/z" value, or as a number of single-mass spectra ? I assume the latter.
I could imagine that matchedFilter never expected spectra with just a single mass. You could fake a second mass, by just repeating the data.
We wanted to try the massifquant peak detection on some of our samples; apparently the findPeaks.massifquant function is not found in the DLL (the R part of the function seems to exist, it seems to fail when calling the DLL...)
I just committed 1.31.8, which enables windows builds of the (experimental) MassIfQuant Peak picker.
The only change I needed (apart from adding the massifquant *.o to OBJECTS in Makevars.win) was to define float64 as double, same as in the unix variant.
there is split() for xcmsRaw objects. Check out ?split.xcmsRaw for the documentation. Basically, you create a vector that is as long as you xcmsRaw has scans, and two values for the LTQ and Orbi scans. You will retrieve a list of two xcmsRaw with only one kind of scans.
Then you can write.cdf or write.mzdata to bring these xcmsRaws back to disk, to read them back in with xcmsSet().
