[BioC] Limma and XML

[Steve Lianoglou]

Hi,

On Fri, Jan 11, 2013 at 9:36 AM, Chen, Wei <chenw at karmanos.org> wrote:
> Hi Steve,
>
> I contact the developer of Limma.  The package does not handle XML format.  Yes, XML is an unusual way to store the data. But I am stuck with 300 files, not a small number. Is there an easy way to parse the XML to excel or txt?

I have no idea of how easy it would be, as I've never seen what this
data looks like.

I suspect this task will, in some sense, be "easy" -- but it will also
likely be extremely tedious.

If you want to get fancy, my guess it that using XQuery is "the right"
way to go, but if you have no experience w/ XQuery, it won't be so
helpful.

My guess is that you may have to end up writing (or getting someone
else to write) some adhoc script that parses the XML files into tables
using your favorite text processing language.

-steve

-- 
Steve Lianoglou
Graduate Student: Computational Systems Biology
 | Memorial Sloan-Kettering Cancer Center
 | Weill Medical College of Cornell University
Contact Info: http://cbio.mskcc.org/~lianos/contact