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rietho / IPO

A Tool for automated Optimization of XCMS Parameters
http://bioconductor.org/packages/IPO/
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Lipidomics set creates warnings about profile mode #26

Closed tobigithub closed 8 years ago

tobigithub commented 8 years ago

Hi, the lipidomics set from the paper creates the following warnings after an IPO experiment. However looking at the data it is actually centroided, so there should be no warning?

### Source (https://health.joanneum.at/IPO/LipidomicsTrainingSet.zip)

library(xcms)

library(Rmpi)

xset <- xcmsSet(method="centWave", peakwidth=c(24.16, 123.5), ppm=10.4, noise=0, snthresh=10, mzdiff=-0.0197, prefilter=c(3, 100), mzCenterFun="wMean", integrate=1, fitgauss=FALSE, verbose.columns=FALSE, nSlaves=32)
xset <- retcor(xset, method="obiwarp", plottype="none", distFunc="cor_opt", profStep=0.66, center=2, response=1, gapInit=0.6976, gapExtend=2.9904, factorDiag=2, factorGap=1, localAlignment=0)
xset <- group(xset, method="density", bw=0.25, mzwid=0.00538, minfrac=0.963, minsamp=1, max=50)

xset <- fillPeaks(xset, nSlaves=32)

Warning messages:
1: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

2: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

3: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

4: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

5: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

6: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

7: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

8: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

9: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

10: In .local(object, ...) :
  It looks like this file is in profile mode. centWave can process only centroid mode data !

Cheers Tobias

glibiseller commented 8 years ago

Hi,

I checked as well in the thermo raw-data and its really centroided. Steffen gave an explanation to this warning in a forum which you can find here.

Cheers, Gunnar