Re: [proteowizard-support] Fwd: R interface to proteowizard ?

[Steffen N. <sne...@ip...>]

Hi Andrew,

XCMS (http://bioconductor.org/packages/bioc/html/xcms.html)
will read any of CDF/mzData/mzXML. Recently I prepared it 
for mzML via pwiz and RAMPAdapter.

You need to compile XCMS yourself, because pwiz is quite large 
and we can't yet include that into bioconductor proper.

You have to download xcms_1.21.15.tar.gz manually,
and run xcms/checkoutpwiz.sh . Next you edit 
xcms/src/Makevars and remove the comment before # $(PWIZOBJECTS)
and # $(PWIZ_LDFLAGS).

The R CMD INSTALL should work as usual.

In case you have questions, don't hesitate to join xcms or xcms-devel,
http://masspec.scripps.edu/xcms/mailinglist.php

Yours,
Steffen

On Tue, 2010-03-09 at 10:27 -0600, Matthew Chambers wrote:
> -------- Original Message -------- 
>                           Subject: 
> [proteowizard-support] R interface
> to proteowizard ?
>                              Date: 
> Fri, 5 Mar 2010 09:35:30 -0500
>                              From: 
> A H <hil...@gm...>
> To: 
> pro...@li...
> 
> 
> Hello list,
>  
> I would like to read mzML-formatted data into R to do analysis


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409