[BioC] Tiling arrays and their probes

[Wolfgang Huber]

Dear Steve,

the CDF structure (i.e. file or package) is only useful if you want to 
analyse cDNA or RNA hybridisation tiling array data for overall mRNA 
abundances using the existing genome annotation. Most people use tiling 
arrays for additional tasks, e.g. transcript discovery and 
"fine-mapping", or ChIP-chip (you didn't say what your use case is).

For ChIP-chip, the "Ringo" package is a good starting point.

For transcript discovery with Affymetrix high density tiling arrays, the 
"tilingArray" package provides  functionality, but it is neither 
comprehensive nor well-standardized. The use cases here are just too 
diverse.

For the mapping of probe sequences to the target genome, the "probeAnno" 
class from Ringo provides a useful container for work in R/Bioc.

If you want to use the mapping provided by Affymetrix, then I think the 
"affxparser" package is a good start point, but for converting its 
output to a "probeAnno" object afaIk you're on your own (perhaps some 
good soul wants to contribute a function for that?)

However, many people prefer to do the mapping themselves. You can use 
exonerate (http://www.ebi.ac.uk/~guy/exonerate), MUMmer 
(http://mummer.sourceforge.net) or the Biostrings package for that. See 
the posToProbeAnno function from Ringo.

  Best wishes
	Wolfgang


------------------------------------------------------------------
Wolfgang Huber  EBI/EMBL  Cambridge UK  http://www.ebi.ac.uk/huber


Steve Lianoglou a écrit 23/04/2008 23:42:
> 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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