xcms

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Dear developers, thank your for the great xcms package. I am trying to use the MS2 data for a fingerprint analysis. My data ([vDIA thermoscientific](https://assets.thermofisher.com/TFS-Assets/CMD/Application-Notes/TN-64283-LC-MS-Veterinary-Drugs-Bio-Matrices-TN64283-EN.pdf)) is very similar to the...

hansenju

Suggest for featureValues()

1

The default column names in output of featureValues() were fileNames(XCMSnExp) and no other options, should there be other options such as sampleNames(XCMSnExp) or customized vector? 

DrRuiLi

connection Error in Biocparallel for chromatogram function

23

We are using Rstudion on a Windows machine and follow the example: [https://bioconductor.org/packages/release/bioc/vignettes/xcms/inst/doc/xcms.html] We succesfully loaded 59 mzML files from an LC-MS run, the step: bpis bpis

tobifuh

xcms3 -- Error in x$.self$finalize() : attempt to apply non-function

17

I got this error when running the following line of code: `bpis

etrh

Error: $ operator is invalid for atomic vectors

1

https://github.com/sneumann/xcms/blob/a0e4c206b4c1f14f34f96282fe0f8dd1023a3917/R/functions-xcmsRaw.R#L302 I think this test should be `if (length(toIdx[inSpectra]) == 1) {` to match the test in binYonX https://github.com/sneumann/xcms/blob/a0e4c206b4c1f14f34f96282fe0f8dd1023a3917/R/functions-binning.R#L261 that shifts between the C functions `binYonX` and `binYonX_mutli` Otherwise you...

arabidopsis

Topic: Looking for help: Dimensions of profile matrices do not match !

6

Hey , I met some problem in using XC MS, I can not fix by myself now. I am looking for help in here. I divided my samples(650 samples) into...

genefisher

how to change tick mark size of y axis on plotChromPeakImage()?

1

There are eight files with a long file name each. The file names were cut off on y axis. How could I change the font size and see the whole...

ghost

Wrong peak picking result using CentWave

4

Hi, I found a very strange issue. When I widen rt range in filterRt(), one peak was no longer picked, and I am not sure whether it is related to...

a1p6ca

readMSdata generate scan error on Mac but not Windows

8

I am trying to run xcms on Mac, however, I am stuck at the first step to import my data. This error does not show up for the example data...

IloveAphid

XCMS set-up

8

Hi I am a beginner in xcms data analysis. I downloaded the latest version of R and installed XCMS and CAMERA package and tried to use them in my data...

Onuh007