[BioC] Tiling arrays and their probes

[Steve Lianoglou]

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