Retention Alignment

[holandir]

Hello,

I have a problem with the retention time alignment of my LC-MS samples.
The "Obiwarp" method works well, but when I try to do the "peakGroups" method, I get the following error:

Error in (function (classes, fdef, mtable) :
unable to find an inherited method for function ‘groupChromPeaks’ for signature ‘"MsExperiment", "PeakDensityParam"’.

This is the line of code I used (mse2 being my MsExperiment data set)

pdp <- PeakDensityParam(sampleGroups = sampleData(mse2)$sample_group, bw = 1.8,
minFraction = 1, binSize = 0.01, ppm = 10)
mse2 <- groupChromPeaks(mse2, pdp)

How can I solve this problem?
I suspect a version-issue.

[jorainer]

yep, this is for sure a version issue. The functionality to use xcms with MsExperiment was added in Bioconductor release 3.18 - so you need at least xcms version 4.0.0 for that. To install these versions you would need a recent R (4.3.2) and then install the respective packages using

install.packages("BiocManager")
BiocManager::install(c("xcms", "MsExperiment"))

There is also some code here and there in this tutorial that is (at present) only available in the current developmental packages (xcms >= 4.1.0). These can at present only be installed through github - but will become the official version in Bioconductor release 3.19 which should be released in April.