Hi, I'm a computational biologist at Genome Sciences Centre, Vancouver, BC, Canada. I'm working on the Affymetrix Human Gene 1.0 ST v1. I'd like to do the normalization, QC report, and fold-change with R. I'm wondering if there is a package in BioConductor for this array. Thanks, Dorothy

Hi Dorothy, There is also an annotation package for this: http://www.bioconductor.org/packages/2.4/data/annotation/html/hugene10 st.db.html Marc dorothyc wrote: > Hi, > I'm a computational biologist at Genome Sciences Centre, Vancouver, > BC, Canada. I'm working on the Affymetrix Human Gene 1.0 ST v1. > > I'd like to do the normalization, QC report, and fold-change with R. > I'm wondering if there is a package in BioConductor for this array. > > Thanks, > Dorothy > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor >

Dorothy. You have a few options in R/BioC: 1. aroma.affymetrix -- see: http://groups.google.com/group/aroma-affymetrix/ http://groups.google.com/group/aroma-affymetrix/web/human-exon-array- analysis (very similar to this) 2. oligo/pdInfoBuilder -- see: http://article.gmane.org/gmane.science.biology.informatics.conductor/1 8963 3. xps -- see: http://www.bioconductor.org/packages/2.3/bioc/html/xps.html Each of these will allow you to do some fairly standard things ... background correct, normalization, RMA summarization, QC plots, etc. Each requires a bit of setup. ... and there are probably others ... Cheers, Mark On 25/11/2008, at 12:17 PM, dorothyc wrote: > Hi, > I'm a computational biologist at Genome Sciences Centre, Vancouver, > BC, Canada. I'm working on the Affymetrix Human Gene 1.0 ST v1. > > I'd like to do the normalization, QC report, and fold-change with > R. I'm wondering if there is a package in BioConductor for this > array. > > Thanks, > Dorothy > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------ Mark Robinson Epigenetics Laboratory, Garvan Bioinformatics Division, WEHI e: m.robinson at garvan.org.au e: mrobinson at wehi.edu.au p: +61 (0)3 9345 2628 f: +61 (0)3 9347 0852

hi, There is a dedicated package available in BioC for exon array analysis. See this - http://bioconductor.org/packages/2.3/bioc/html/exonmap.html {BioC page for 'exonmap'} An article demonstrating its use - http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.0040 006 cheers.. amit On Tue, Nov 25, 2008 at 6:47 AM, dorothyc <dorothyc@bcgsc.ca> wrote: > Hi, > I'm a computational biologist at Genome Sciences Centre, Vancouver, BC, > Canada. I'm working on the Affymetrix Human Gene 1.0 ST v1. > > I'd like to do the normalization, QC report, and fold-change with R. I'm > wondering if there is a package in BioConductor for this array. > > Thanks, > Dorothy > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- --------------------------------------------------------------- The robbed that smiles, steals something from the thief. - Shakespeare --------------------------------------------------------------- [[alternative HTML version deleted]]