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Topic: unable to create xcms object (Read 5903 times) previous topic - next topic

unable to create xcms object

Dear All,

I have been trying to create xcms object using the command
Code: [Select]
xset <- xcmsSet()
after changing the directory to where my CDF files is. I got the following error:
"Error in logical(nrow(m)): invalid 'length' argument"
This is if I tried to process the positive data. When I tried to process the negative spectra, I got the following error:
"error in rmat[,"rt"]:incorrect number of dimensions. Any idea what happen? Thanks in advance for your help.

The following is the traceback associated with the error in rmat.
Code: [Select]
> traceback()
8: .local(object, ...)
7: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
6: findPeaks.matchedFilter(<S4 object of class "xcmsRaw">)
5: do.call(method, list(object, ...))
4: .local(object, ...)
3: findPeaks(lcraw, ...)
2: findPeaks(lcraw, ...)
1:
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252 
[2] LC_CTYPE=English_United States.1252   
[3] LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] multtest_2.12.0 Biobase_2.14.0  xcms_1.32.0     mzR_1.2.2      
[5] Rcpp_0.9.13    

loaded via a namespace (and not attached):
[1] codetools_0.2-8  MASS_7.3-19      splines_2.15.1   stats4_2.15.1   
[5] survival_2.36-14 tools_2.15.1 

Re: unable to create xcms object

Reply #1 –
The reason is that no peaks could be detected in your samples with these settings.

You could try modifying the feature detection parameters and/or using the centWave method.
Since you didn't tell us what instrument you are using it is hard to give any further advice.

Ralf

Re: unable to create xcms object

Reply #2 –
Ralf, thank you so much for your help. These data were generated using waters instrument.
Can you suggest on initial parameter I should try? What command I should use?
I only know xcmsSet following the xcms demo.
This is my first time looking at metabolomics data.

Re: unable to create xcms object

Reply #3 –
Waters Q-TOF ?

For a start, I'd suggest you try processing your data using XCMS Online with the "HPLC /  Waters Q-TOF" parameter set.

Re: unable to create xcms object

Reply #4 –
It's actually Waters UPLC/QTOF-MS
I tried xcms online with UPLC/Q-TOF parameter settings. I was not able to run it as is. I need to turn off the retention time correction to be able to run it. I guess I need to learn more about this to understand why it didn't work with retention time correction.

Now, how do I translate it to xcms in R? I have too many files to do it online.

Also, is there a documentation on how to see the quality of these data in general.

Thank you

Re: unable to create xcms object

Reply #5 –
For those wondering,

I was able to run xcmsSet using the following command:
xset <- xcmsSet(method="centWave")