Hi All! I am a beginner and am currently trying to formulate a BioC workflow for some affymetrix datasets (human, rat, mouse). I have been reading about probe remapping- have come across AffyProbeMiner, Cleaner and GATExplorer-does anyone have experience with these? Is remapping important even for the latest BioC versions-have the CDFs been redefined already? (How) does it affect choices of normalization/summarization algorithms? Thank you much... Best, Swapna School of Computational & Integrative Sciences JNU, Delhi [[alternative HTML version deleted]]

Hi, On Fri, Nov 19, 2010 at 4:57 AM, Swapna Menon <swapna30 at="" gmail.com=""> wrote: > Hi All! > > I am a beginner and am currently trying to formulate a BioC workflow for > some affymetrix datasets (human, rat, mouse). I have been reading about > probe remapping- have come across AffyProbeMiner, Cleaner and > GATExplorer-does anyone have experience with these? Is remapping important > even for the latest BioC versions-have the CDFs been redefined already? > (How) does it affect choices of normalization/summarization algorithms? > > Thank you much... Try poking around here first before you take on that burden: http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/gen omic_curated_CDF.asp -- Steve Lianoglou Graduate Student: Computational Systems Biology ?| Memorial Sloan-Kettering Cancer Center ?| Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact