Dear List, I'm new to microarray analysis and need to calculate gene signal from samples. The tab-delimited file has been prepared and the signal for each probe is calculated. My question is: 1) How to filter the probes those are disqualified? 2) How to calculate the gene signal from probe signal? The reflection from probes to genes are clear but I have no idea if I need to simply sum up all the probes of a given gene or something else. Thanks a lot and best wishes. -- Lv Yang School of Life Sciences Sun Yat-Sen University Guangzhou, 510275, Guangdong P. R. China [[alternative HTML version deleted]]

Dear Yang, The easiest way I know if you are starting out is the AffylmGUI and oneChannelGUI programs., oneChannelGUI is the more powerful of the two., but AffylmGUI has more detailed on line turoials with test cases. Working through teh worked examples will answer your questions. I can also send you my course material off-line on the theory if it will help. Best wishes, Rich On Jun 17, 2010, at 10:13 AM, Yang Lv wrote: > Dear Richard, > > It's Affymetrix. > > On Thu, Jun 17, 2010 at 9:16 PM, Richard Friedman <friedman at="" cancercenter.columbia.edu=""> > wrote: > Dear Yang, > > What kind of array are you using (Affymetrix, 2 color etc)? > > Best wishes, > Rich > ------------------------------------------------------------ > Richard A. Friedman, PhD > Associate Research Scientist, > Biomedical Informatics Shared Resource > Herbert Irving Comprehensive Cancer Center (HICCC) > Lecturer, > Department of Biomedical Informatics (DBMI) > Educational Coordinator, > Center for Computational Biology and Bioinformatics (C2B2)/ > National Center for Multiscale Analysis of Genomic Networks (MAGNet) > Room 824 > Irving Cancer Research Center > Columbia University > 1130 St. Nicholas Ave > New York, NY 10032 > (212)851-4765 (voice) > friedman at cancercenter.columbia.edu > http://cancercenter.columbia.edu/~friedman/ > > In Memoriam, > George Scithers > > > > > On Jun 17, 2010, at 12:22 AM, Yang Lv wrote: > > Dear List, > > I'm new to microarray analysis and need to calculate gene signal from > samples. The tab-delimited file has been prepared and the signal for > each > probe is calculated. My question is: 1) How to filter the probes > those are > disqualified? 2) How to calculate the gene signal from probe signal? > The > reflection from probes to genes are clear but I have no idea if I > need to > simply sum up all the probes of a given gene or something else. > > Thanks a lot and best wishes. > > -- > Lv Yang > > School of Life Sciences > Sun Yat-Sen University > Guangzhou, 510275, Guangdong > P. R. China > > [[alternative HTML version deleted]] > > > _______________________________________________ > 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 > > > > > -- > Lv Yang > > School of Life Sciences > Sun Yat-Sen University > Guangzhou, 510275, Guangdong > P. R. China

On Jun/17/10 6:22 AM, Yang Lv wrote: > Dear List, > > I'm new to microarray analysis and need to calculate gene signal from > samples. The tab-delimited file has been prepared and the signal for each > probe is calculated. My question is: 1) How to filter the probes those are > disqualified? 2) How to calculate the gene signal from probe signal? The > reflection from probes to genes are clear but I have no idea if I need to > simply sum up all the probes of a given gene or something else. > > Thanks a lot and best wishes. > Dear Yang have a look at the exercise book http://www.bioconductor.org/pub/biocases/ that discusses your questions in extenso. Best wishes Wolfgang