[BioC] Affymetrix Yeast Tiling Arrays

[Steve Lianoglou]

Hi,

On Sep 9, 2008, at 10:57 AM, Paco Recca wrote:

> Hello!
>
> I am planning to run and analyze some Affy Yeast tiling arrays. Is  
> bioconductor offering some tools for this specific platform?


Have a look at the tilingArray package:
http://www.bioconductor.org/packages/2.2/bioc/html/tilingArray.html

and its two references:
(1) Experimental:
Lior David, Wolfgang Huber, Marina Granovskaia, Joern Toedling, Curtis  
J. Palm,
Lee Bofkin, Ted Jones, Ronald W. Davis, and Lars M. Steinmetz A high- 
resolution
map of transcription in the yeast genome. PNAS, 2006. 8, 9, 10

(2) Methods:
Wolfgang Huber, Joern Toedling and Lars M. Steinmetz Transcript  
mapping with
oligonucleotide high-density tiling arrays. Bioinformatics, 2006. 9, 11

The davidTiling package contains the data for reference (1)
http://www.bioconductor.org/packages/release/data/experiment/html/davidTiling.html

Although it most likely won't be a 1:1 application from the package to  
your application, these are worthwhile references to start reading and  
wrapping your brain around what you might have to do.

Note that their normalization technique requires hybridization of  
genomic DNA to a chip ... you say you are planning to run the arrays,  
so assuming you can include this in your analysis, you actually might  
be able to use the tilingArray package pretty much out of the box.

All of the above advice should actually be predicated with "Assuming  
you want to do some type of transcriptome mapping ..."

If you're using the tiling array for something like ChIP-chip, then  
this advice won't be of much help at all, and other packages like  
Ringo and oligo might be a good place to start looking.

--
Steve Lianoglou
Graduate Student: Physiology, Biophysics and Systems Biology
Weill Cornell Medical College of Cornell University

http://cbio.mskcc.org/~lianos