XCMS
From Metlin Wiki
Contents |
[edit] General
The xcms package reads and processes LC/MS data stored in NetCDF (AIA/ANDI), mzXML, and mzData files. It includes numerous options for visualizing and interacting with that data. In addition, it includes functionality for peak picking, non-linear retention time alignment, and relative quantitation. It is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples.
[edit] Download
XCMS is part of the official Bioconductor project. Please see http://www.bioconductor.org/download/ Since the XCMS version is tied to the Bioconductor release which in turn is tied to your installed R version, you'll potentially obtain an outdated XCMS. Since XCMS runs with any R >= 1.9, it is recommended to check if the latest stable XCMS version is installed.
[edit] FAQ
Some questions (and their answers) appear on the xcms mailing list quite often, so here is a collection of Frequently Answered Questions:
[edit] CookBook
The vignettes in the package give a brief tutorial over the whole process of analysing MS data with XCMS.However, everybody and the mailing list has a few tricks, which are not suitable for the manpages, but worth sharing.
This section also includes known-to-work parameter sets for a range of mass spectrometers.
[edit] Related Software
- DAnTE helps users to perform various downstream data analysis, data reduction, and data comparison steps. DAnTE includes a graphical environment for visualizing the data during the processing steps. DAnTE can associate one or more "factors" with each dataset, which are then taken into consideration during the data processing.
- Picasa can be used to view the xic's png files and is pretty slick as I can search for the XIC numbers, add stars and comments and export to the web. For examples see Brett's Public Gallery He has also added some comparisons he's done between SIEVE a similar program from Thermo and xcms in this picasa folder
[edit] For Developers
XCMS is developed by a team of developers around the world. The current stable version is Bioconductor 2.3 The next stable version will be released with Bioconductor 2.4 which currently has no schedual but we're expecting release to beMay
The following links will be helpful examining the current state of the XCMS development:
- Dataset faahKO
- Dataset collection of raw data
We currently implementing new features for the October release, then we'll have to do:
- writing the release notes
