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Topics - cpudney

1
CAMERA / Possible bug when groupCorr called with xraw argument
G'day,

When calling groupCorr with the xraw argument set I see the following error message:

Code: [Select]
> groupCorr(object=yanGI, calcIso=TRUE, xraw=xcmsRaw(file))
Start grouping after correlation.
Error in peaks(xa@xcmsSet) : 
  error in evaluating the argument 'object' in selecting a method for function 'peaks': Error: object 'xa' not found

Looking at the source code in fct_groupCorr.R it appears the xa has not been assigned a value.

Code: [Select]
  # Check LC information and calcCorr was selected
  if(calcCiS && object@xcmsSet@peaks[1,"rt"] != -1){
    if(!is.null(xraw)) {
      #Use provided xcmsRaw
      maxscans <- length(xraw@scantime)
      scantimes<-list();
      scantimes[[1]] <- xraw@scantime
      pdata <- peaks(xa@xcmsSet)
      EIC <- CAMERA:::getEICs(xraw,pdata,maxscans)

Is this a bug?

Regards,
Chris.
2
XCMS / Should findmzROI be sensitive to m/z values?
G'day,

We've been using findPeaks.centWave to process individual chromatograms, see this thread.  We use this script:

Code: [Select]
require(xcms)
xdata <- read.csv(file="chrom.csv", header=TRUE, sep=",")
rtSec <- xdata$RT
numPoints <- length(xdata$I)
xraw <- new("xcmsRaw")
xraw@tic <- xdata$I
xraw@scantime <- rtSec
xraw@scanindex <- 1:numPoints
xraw@env$mz <- rep(130.61, numPoints)
xraw@env$intensity <- xdata$I
xpeaks <- findPeaks.centWave(xraw, peakwidth=c(10,200), ppm=0, mzdiff=0, snthresh=0, integrate=1, prefilter=c(0,0), verbose=TRUE)
plot(xdata$RT, xdata$I, type='l')
for (i in 1:nrow(xpeaks)) {
 lines(xdata[findInterval(xpeaks[i,'rtmin'],rtSec):findInterval(xpeaks[i,'rtmax'],rtSec), c('RT','I')], col=rainbow(16)[i], type='h')
}
prmatrix(xpeaks)
When processing a single chromatogram, all points are given the same m/z value, in the example above it's 130.61.

However, I noticed that if you change this value you get different results.  This seems to arise from the ROI detection step, which can produce different numbers of ROI depending on the m/z value of the chromatogram.  For example, for the attached data and m/z of 136.01 it finds 12 ROIs.  If the m/z is changed to 13.061 then it finds 23 ROIs.

I don't understand why this should be; if all the m/z values of a chromatogram are identical then they should form the same set of ROIs regardless of the m/z value.

I've looked at the source code for findmzROI and I can't see any problem (but haven't the capacity to debug it).

Is the behaviour I'm observing correct?

Thanks,
Chris.

[attachment deleted by admin]
3
XCMS / How to run findPeaks.centWave on an individual chromatogram
G'day,

I was experimenting earlier today with using findPeaks.centWave on a single chromatogram.

The chromatogram was stored in a CSV file (RT, I) and I passed it to findPeaks.centWave thus:

Code: [Select]
require(xcms)
data <- read.csv(file="chrom.csv", header=TRUE, sep=",")
numPoints <- length(data$I)
raw <- new("xcmsRaw")
raw@tic <- data$I
raw@scantime <- data$RT
raw@scanindex <- 1:numPoints
raw@env$mz <- rep(136.061, numPoints)
raw@env$intensity <- data$I
peaks <- findPeaks.centWave(raw, peakwidth=c(0,100))

Actually, it must have been something like the above because it worked - it detected a peak in precisely the right spot - but now that I try the above again it fails to find a single ROI and so bails out.

Is the above (or something similar) the correct approach for passing a single chromatogram to findPeaks.centWave?

I've attached chrom.csv.

Thanks,
Chris.
4
XCMS / Can/should we use findPeaks.centWave with profile/continuous
G'day,

We are interested in using findPeaks.centWave with profile/continuous data but note that it expects centroided data.

Is this a strict requirement?  Are there parameter settings that would make it possible to use centWave with profile data?

We're keen to preserve mass accuracy.

Thanks,
Chris.