Problem with XCMS
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Titan • 0
@titan-9461
Last seen 3.0 years ago
USA
Hey,
I tried to work on XCMS2. With the same script below xcms was working well. Now when I try to work on it, it gives me following error. Can anyone help me to troubleshoot the problem. 

> source("http://bioconductor.org/biocLite.R")
Bioconductor version 3.2 (BiocInstaller 1.20.1), ?biocLite for help
> library(xcms)
> library(mzR)
> library(msdata)
> setwd("C://Users/Manoj/Desktop/trial_xcms/")
> list.files()
[1] "data_processing_XCMS.txt"         "global_positive_Batch2_E67.mzXML"
> mzdatafile <- list.files(pattern="global_positive_Batch2_E67.mzXML", recursive=TRUE, full.names=TRUE)
> xraw <- xcmsRaw(mzdatafiles[2], includeMSn + TRUE)
Error in xcmsSource(filename) : 
  error in evaluating the argument 'object' in selecting a method for function 'xcmsSource': Error: object 'mzdatafiles' not found
> 

 

Thank you.

xcms metabolomics lipidomics proteomics massspectrometry • 1.1k views
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@james-w-macdonald-5106
Last seen 11 hours ago
United States

Any time you get an error saying something like

Error: object 'mzdatafiles' not found

This is a huge red flag that you have made a mistake, rather than some bug. R is saying 'Hey, you told me to use this thing, but I can't find it'. And the reason for that is usually a typo - in this case, the object you are trying to use is called mzdatafile, not mzdatafiles.

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Titan • 0
@titan-9461
Last seen 3.0 years ago
USA

Thanks dude. I did not check that :)

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Entering edit mode
Titan • 0
@titan-9461
Last seen 3.0 years ago
USA

Thanks dude. I did not check that :)

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