Hello! I am planning to run and analyze some Affy Yeast tiling arrays. Is bioconductor offering some tools for this specific platform? Thank you very much -paco __________________________________________________ spazio gratuito per i tuoi file e i messaggi [[alternative HTML version deleted]]

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/davi dTiling.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