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Messages - johannes.rainer

31
XCMS / Re: export XCMS2 fragments
We're actually currently implementing some potentially interesting stuff. In the next version you'll have a featureSpectra and chromPeakSpectra function that returns MS2 spectra related to a feature or chromatographic peak.

stay tuned.
32
XCMS / Re: replacement for getEIC in XCMS3
Dear Krista,

I realized that that's something apparently missing in xcms version 3 at present. I will think of a solution and post it. Thanks for the feedback.

cheers, jo
33
XCMS / Re: No console messages xcmsSet (xcms v1.50.1)
Got now an explanation from Martin Morgan (https://support.bioconductor.org/p/96856/). Basically, you could use the progressbar, but you have to increase the number of tasks, so that the progress bar will be updated more frequently. Note however that a) the number of tasks should not be larger than the number of files you're processing and b) there might be a performance decrease with too many tasks.
So, in your case you could:
Code: [Select]
library(faahKO)
library(xcms)
library(BiocParallel)
library(snow)

## The directory with the NetCDF LC/MS files
cdfpath <- file.path(find.package("faahKO"), "cdf")

setwd(cdfpath)

## Register the parallel processing setting - will be used by default by all xcms methods
## Set tasks to a reasonable number
register(SnowParam(tasks = 10, progressbar = TRUE))

peakmatrix <- xcmsSet()

Now, for your 400 file experiment you might want to increase the number of tasks to get more frequent callbacks and updates of the progress bar.

Hope this helps.

cheers, jo
34
XCMS / Re: No console messages xcmsSet (xcms v1.50.1)
Dear Will,

with the switch to BiocParallel the progress information are no longer printed immediately - this seems to have to do with the way BiocParallel handles the sub-processes. I know that is annoying, but there is not much we can do within xcms.

I'll get in contact with the BiocParallel developers to check if we can fix that.

cheers, jo