Open v-v1150n opened 3 months ago
Which versions of the packages are you using? could be that you use an old version of xcms.
My xcms package version is:
packageVersion("xcms") [1] ‘4.3.1’
I see, no, indeed, you are right. The use of FillChromPeaksParam
is no longer supported with XcmsExperiment
. This method notoriously underestimated the gap-filled data, thus it is highly suggested to use the ChromPeakAreaParam
instead, that integrates the data from the m/z-rt ranges of the actually identified chromatographic peaks.
But note that I have also just recently implemented the possibility to change from a XcmsExperiment
to XCMSnExp
object - if you really want to apply the old method. This can be done with xdata <- as(xdata, "XCMSnExp")
after installing the current xcms version from my branch (i.e. using BiocManager::install("sneumann/xcms", ref = "jomain")
.
The following are the steps I took to analyze GC-MS. When it comes to FillChromPeaksParam, this function requires the use of
XCMSnExp
objects. The objects I use in the fifth step will beXcmsExperiment
objects. I don’t know if there is any way to handle the conversion of objects, or Are there any suggestions for optimization steps?