XCMS error message and Q about MZmine

[Jamie]

Hey,

I'm absolutely horrible with computer stuff and my boss has me
attempting to use some of the proteomics software thats
available..MZmine and XCMS. However, I've been unsuccessful at
setting up either one of those. When setting up a data set in xcms i
receive this error message :Error in rmat[, "rt"] : incorrect number
of dimensions
I've gotten XCMS to successfully get past this point once (using only
0-1500 m/z range). The error occurs when I put in data thats from the
150-4000 m/z range. I'm not exactly sure what the error message
means, nor how to fix it or if the m/z range difference is just a
coincidence...any thoughts?

As for MZ mine, I've successfully uploaded the raw file, looked at the
spectra and the chromatogram, however I cannot figure out how to make
a peak list successfully. It shows up under the peaklist header, but
there's no info in the table. I can't figure out whether I'm doing
something retarded and not converting it right or whether I have other
issues..

Thanks for your time...any thoughts would be greatly apprecciated..
and i'm sure my advisor would be thrilled as well.

:-) Have a good day

[Natalie Tasman]

Hi there Jamie,

Just to be clear, the two programs that you mentioned aren't from the Seattle Proteome Center (SPC), and you might find more support if you write directly to those programs' maintainers.  But if anyone else on the list has experience, of course they are welcome to respond here.

Best wishes,

Natalie