[BioC] cdfenv files ATTN: James McDonald

[Benilton Carvalho]

Andrew,

you will need some auxiliary packages available at:

http://www.biostat.jhsph.edu/~bcarvalh/old/research.html

and whenever you need anything regarding oligo, you can email me and  
i'll be happy to help you.

b

On Sep 22, 2006, at 9:57 AM, Andrew Van Brunt wrote:

> 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
>
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