[BioC] Tiling arrays and their probes

[Naira Naouar]

Hi Steve,

You will need to install the CDF you created by doing:
R CMD INSTALL pd.dm35b.mf.v02.3.bdgpv4h***.tar.gz  -l /path/to/RLIB

Then loading this package by using

library(pd.dm35b.mf.v02.3.bdgpv4h)

should be fine.

About mapping probes to genomic positions, you can find some hints on 
how to do this in this paper: 
http://www.sciencemag.org/cgi/content/abstract/317/5836/338

Best,
Naira


Steve Lianoglou wrote:
> Hi all,
>
> I'm trying to get my feet wet analyzing data from the affymetrix  
> drosophila v1 tiling array[1].
>
> I've been poking around in the vignettes for the `oligo` package, and  
> the `tilingArray` package, but I'm having a few problems.
>
> The first thing I'd like to do is to be able to map my probes back to  
> their appropriate genomic position. I gather that this information is  
> buried in the *.bpmap file that is in the library file for my tiling  
> array[2]. Unfortunately for me, this is in some binary format. If I've  
> understood some of the things I've tripped over while browsing the  
> archives for this mailing list, I need to construct a CDF file for the  
> array, is this correct?
>
> I've found some previous emails on this list about constructing a CDF  
> from the appropriate library files, and all roads seem to point to a  
> post by Naira[3].
>
> Trying to follow these instructions, I downloaded the library files  
> for my tiling array[2] and ran the `makePDpackage` while pointing to  
> what I assume are the correct *.bpmap and *.cif files that I found  
> buried in the d/l'ed libraries. This step seems to work and created a  
> working set of files in a `pd.dm35b.mf.v02.3.bdgpv4h` directory.
>
> I then tried to run the R CMD's to build the cdf using the appropriate  
> name generated from the `makePDpackage` library, but this gives me a  
> *.tar.gz file that I don't really know what to do with. I've tried  
> unzipping this file and telling R to load it as a library file with  
> `library(pd.dm35b.mf.v02.3.bdgpv4h)` but it seems I may need to  
> install it some other way because R can't find "that package." This  
> makes sense, but I don't really know what to do to install this CDF,  
> or if this is the CDF file that I'm after at all.
>
> Trying a different approach, I've been able to load the bpmap file  
> through the affyio package like so:
>  > bpmap <- .Call('ReadBPMAPFileIntoRList',  
> 'Dm35b_MF_v02-3_BDGPv4h.bpmap')
>
> But I'm trying to poke around the bpmap data struct I get in return,  
> and I'm not really finding what I'm after.
>
> If anybody has experience working w/ such tiling arrays, could you  
> please point me in the right direction? There are several rabbit holes  
> that I find myself going down, a hint at which one to best commit to  
> would be great. More info about mapping probes to genomic positions  
> would be great as well.
>
> Thanks for your time,
> -steve
>
> [1] http://www.affymetrix.com/products/arrays/specific/drosophila_tiling1_0r.affx
> [2] http://www.affymetrix.com/products/arrays/specific/drosophila_tiling1_0r.affx 
>   (there is a "Library Files" link on the right)
> [3] http://article.gmane.org/gmane.science.biology.informatics.conductor/16041/match=bioconductor+tiling+array
>
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-- 
==================================================================
Naira Naouar 

Tel:+32 (0)9 331 38 63                      
VIB Department of Plant Systems Biology, Ghent University
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nanao at psb.ugent.be                         http://www.psb.ugent.be