[BioC] cdfenv files ATTN: James McDonald

[Andrew Van Brunt]

Hello -

I am almost embarrassed to be posting to this list since my R programming
skills are essentially non-existent and my computer skills in general a
probably quite lacking compared to others on this list. But I have been
banging my head on the wall for too long now so I figured I better suck it
up and post.

I apologize in advance for the length of this message but as I said, I am
a very naive user and I have lots of questions and I also want to present
some evidence that I've been trying my best to find the answers before
posting to the list. And the subject does contain James McDonald but thats
because he seems to reply to questions of this nature and thus seems to be
something of an expert on this topic but really anyone's help would be
appreciated.

The problem I have is we are attempting to use R/BioC to analyze some
affymetrix SNP chip data. Specifically, we have .cel files and the chip
used was the Human Mapping 250K_Sty array. Basically, I need to be able to
associate the probe intensity values with the proper probes. I know this
can be done with Affy software but we have hundreds of chips and you can
not export probe intensity tables from programs like GTYPE except 10 at a
time, so that would be very labor intensive. In the future we may have
many hundreds or even thousands of chips to analyze and point and click
will not be an acceptable solution.

So basically my question is this:
I need a package that will associate the correct intensities with the
probe names for further analysis. It doesn't seem that there are really
any packages for doing this with any mapping arrays as most array analyses
through BioC (it seems to me anyways) are concerned with expression
arrays. Are there packages for Mapping arrays?
here is what I have learned/tried so far:

visiting this thread ->
http://article.gmane.org/gmane.science.biology.informatics.conductor/4195/match=chip+libraries

I learned that not all cdfenv files are listed for download on the BioC
site. So I tried the recommended solution here using reposTools, only my
menu does not look like the one posted and there is not an option for the
CDF Environment Repository. I think this was a pretty old recommendation.
So does anyone know how I can see those that are not on the BioC website?

Have also read several threads and the documentation for makecdfenv and I
am unfortunately on R for windows and I think I have the windows binary as
opposed to the source code installed. I've read about the extra tools and
Perl you have to download and all this other stuff and its all very
confusing to me - needless to say I've tried to make my own library but
have had no such luck. I even have problems installing the Active perl for
windows in the right location etc. I've tried using cygwin and not had
much luck there either. So what I really need is a zipped windows binary
package that I can install for the Mapping_250K_Sty chip so I can read
those cel files and work with the probe intensities. So if anyone knows
where I can find one please let me know. Or if anyone would be willing to
make one for me they would have my eternal gratitude. I guess lastly, if
anyone would be willing to walk a real computer novice on how to make the
environment and create a windows binary package out of it (so I can port
it to other windows machines) that would be appreciated too... not as much
perhaps and just giving me a package to download but appreciated
nonetheless.

Any takers?
Any ideas?
Any suggestions?

Thanks,
Andrew Van Brunt
Division of Statistical Genomics - Washington University in St. Louis

reply to: andrew at dsgmail.wustl.edu