Dear All,
I have been trying to create xcms object using the command
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.
> 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
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
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.
Waters Q-TOF ?
For a start, I'd suggest you try processing your data using XCMS Online (http://https://xcmsonline.scripps.edu/) with the "HPLC / Waters Q-TOF" parameter set.
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
For those wondering,
I was able to run xcmsSet using the following command:
xset <- xcmsSet(method="centWave")