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fillPeaks() ERROR

Hi all,
I am trying to reproduce locally some results I have obtained using XCMS online.
My input files are .mzdata.xml files generated with Agilent MassHunter Qualitative analysis B.05.00.
The first steps : peak extraction (xcmsSet()), grouping (group()), retention time correction (retcor()), grouping (group()) work fine.
However, I get an error message when I execute the fillPeaks() function as follow:

Error in seq.default(floor(mrange[1]/step) * step, ceiling(mrange[2]/step) *  : invalid (to - from)/by in seq(.)

I looked for solutions on the web without success.
I hope that you will be able to help me.
Thank you in advance

I am using:
R version 3.0.1 (2013-05-16)
Platform: x86_64-w64-mingw32/x64 (64-bit)
xcms_1.36.0
Biobase_2.20.1
BiocGenerics_0.6.0
mzR_1.6.2
Rcpp_0.10.4

Re: fillPeaks() ERROR

Reply #1
blk.desperado,

A couple of things, I don't think that xcmsOnline is using the latest xcms version. You should check and see what version it was run under. The next thing is that it's a bit odd that this happened during the fillPeak process as I would expect if you were going to have this error that it would come up at the first command. What file does it get to? Can you load this file up by itself and have a look with:

Code: [Select]
library(xcms)
xr<-xcmsRaw("Name of Last file loaded")
xr

Also worth a try, (bad solution) change the grouping parameters post-retcor. See if this makes a difference.

Cheers,

Paul
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page

Re: fillPeaks() ERROR

Reply #2
Hi Paul,
I changed the grouping parameters post-retcor and it solved the problem. Not sure to understand what happened here.
Anyway, thank you
Cheers

Re: fillPeaks() ERROR

Reply #3
The error comes from the binning of the LC-MS file. Basically it had problems loading the file and then binning it. Its something to do with the bin size and the size of the group in m/z, if I remember correctly.

If it happens again I might ask you for files to take a look.

Cheers,

Paul
~~
H. Paul Benton
Scripps Research Institute
If you have an error with XCMS Online please send me the JOBID and submit an error via the XCMS Online contact page