User of R xcms/metaMS packages?

[dav7841]

Hi all, I'm looking into using new software packages to process GCMS data. We a have a few systems in our lab (varian, shimadzu, Agilent) and I have a good bit of experience in using their relative software. Only a big issue for us is the data processing time. I work in a flavour chemistry lab and carry out unknown analyses of headspace compounds. I've been looking into pipeline methods of analyses that use R, which are predominantly used in proteomics and such, and feel these type of workflows could solve our problems.
My problem with these is my lack of experience using R. I have been spending time teaching myself and looking up online tutorials. I also plan on taking a course as soon as my company would arrange it. In the meantime in the hopes of speeding up my learning, I wonder if anyone could help me with this. As the title suggest I'm interested in xcms and metaMS packages of R. I'm starting to become somewhat familiar with these and am very interested to hear from anyone who uses these packages in their daily routine.
Even if someone would just post a screen shot of their string window from a normal sample run that would be great!
I'd appreciate any help I can get with this, thanks.

[lmh]

I use XCMS for comparison of unknowns, and to produce PCA plots, but in a very amateurish way. Do you have a way you can be contacted? XCMS works quite well on GC-MS data, but the default peak-widths will be far too wide. I am absolutely not an expert though, and may be out-of-date (I use only the local version, not the online version)

[dav7841]

Hi, thanks for the reply. I'll take whatever help I can get! so anything you can tell me will be much appreciated. My email is david.mannion@teagasc.ie. Like I said I'm starting to become familiar with the process but still have a ways to go. Do you use NIST matching for your unknowns or a user lib? or both? one of the things I'm stuck on at the moment is trying to do a search against NIST. I have a user database set up and can do a search against that but that's it so far. If it's possible would you be able to send me on your script window from R?So I can see what your typical workflow is.

[lmh]

You should have mail! I'm afraid for me the step between finding interesting peaks in XCMS and identifying them by library comparisons is manual...
I've sent you a document that explains our work-flow in XCMS/R, but we're not the most sophisticated users. R is incredibly powerful, though. One thing I haven't explored with it is setting up a script for PLS-DA (partly through lack of time, and partly because it's hard to get people to do adequate replication).

[dav7841]

Thanks a million for this, I'll go over what you sent this evening after work. I've never been this excited to do some homework lol

[iluvgc]

Thanks a million for this, I'll go over what you sent this evening after work. I've never been this excited to do some homework lol

Hi

I am in a similar situation as yours, like I have GCMS datasets which I am interested in analyzing using MEtaMS packagae. I see that you were trying to do something similar ...Did you have any luck...Were you able to analyse datasets. Please can you help me get started. Thanks...

[iluvgc]

You should have mail! I'm afraid for me the step between finding interesting peaks in XCMS and identifying them by library comparisons is manual...
I've sent you a document that explains our work-flow in XCMS/R, but we're not the most sophisticated users. R is incredibly powerful, though. One thing I haven't explored with it is setting up a script for PLS-DA (partly through lack of time, and partly because it's hard to get people to do adequate replication).

I am in a similar situation as dav7841, like I have GCMS datasets which I am interested in analyzing using MEtaMS packagae. I see that you were previously doing something similar and group seperation..which would be good enough for me to see if there is any difference ...Please can you help me get started. you can email me bpvaith@gmail.com...Thanks...