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Question: Problem with XCMS
0
gravatar for Titan
22 months ago by
Titan0
USA
Titan0 wrote:
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.

ADD COMMENTlink modified 22 months ago • written 22 months ago by Titan0
0
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald45k wrote:

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.

ADD COMMENTlink written 22 months ago by James W. MacDonald45k
0
gravatar for Titan
22 months ago by
Titan0
USA
Titan0 wrote:

Thanks dude. I did not check that :)

ADD COMMENTlink written 22 months ago by Titan0
0
gravatar for Titan
22 months ago by
Titan0
USA
Titan0 wrote:

Thanks dude. I did not check that :)

ADD COMMENTlink written 22 months ago by Titan0
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