Moving over from xcms issue #430

[Phylloxera]

Thanks @cbroeckl for all the help so far, RC <- ramclustR(xcmsObj = xdata, ExpDes=experiment)

Error in if (!is.null(xcmsObj) & mslev == 2 & any(is.null(MStag), is.null(idMSMStag), : missing value where TRUE/FALSE needed In addition: Warning message: In ramclustR(xcmsObj = xdata, ExpDes = experiment) : NAs introduced by coercion

Is this because I filled in something incorrectly at experiment <- defineExperiment(csv = FALSE)?

[cbroeckl]

use:

cat(experiment) and report the output to the console here please

[Phylloxera]

Error in cat(experiment) : argument 1 (type 'list') cannot be handled by 'cat'

[cbroeckl]

sorry just type experiment

[Phylloxera]

$design Value Experiment separate_broeckling1 Species sus Sample serum Contributor usmarc platform LC-MS Description Experiment experiment name, no spaces Species species name Sample sample type Contributor individual and/or organizational affiliation platform GC-MS or LC-MS

$instrument value chrominst Waters_Acquity_UPLC msinst Waters_XevoG2 column C8 solvA 5%MetOH solvB 95%MetOH CE1 6 CE2 30 mstype mse msmode positive ionization positive colgas nitrogen msscanrange 50-1200 conevolt 2200 MSlevs 1,2

[cbroeckl]

## first we will change MSlevs to 2
fix <- which(row.names(experiment[[2]]) == "MSlevs")
experiment[[2]][fix,1] <- 2

then when you run ramclustR:

RC <- ramclustR(xcmsObj = xdata, ExpDes=experiment, MStag = "01.mzML", idMSMStag = "02.mzml")

[Phylloxera]

I changed the command slightly (i must have misread your naming scheme)

RC <- ramclustR(xcmsObj = xdata, ExpDes=experiment, 
                MStag = "ms1.mzML", idMSMStag = "ms2.mzml")

And it seems to have ran, thanks!

organizing dataset normalizing dataset calculating ramclustR similarity: nblocks = 3 1 2 3
RAMClust feature similarity matrix calculated and stored: RAMClust distances converted to distance object fastcluster based clustering complete dynamicTreeCut based pruning complete RAMClust has condensed 2971 features into 544 spectra collapsing feature into spectral signal intensities writing msp formatted spectra msp file complete

[hechth]

@Phylloxera so you can confirm that this problem was fixed? Then we can actually close this here :)

Thanks!