Hi all.. i have following questions. 1) How many probesets represent a gene on microarray chip ? 2) How do i access raw intesity value of probes (before normalization) ? 3) Do i need to read cdf file to do that ?? 4) After pre-processing the data and normalization, we generally go for significance tests and gene grouping. My question is, if i group the genes before performing significance test (say now i have 3 groups based on apoptosis,cell cycle, DNA replication) and then perform significance test within each group, will the results be same as that of conventional way ?? Is it a valid method to do so?? Sorry if my questions are silly. -- output of sessionInfo(): --NONE-- -- Sent via the guest posting facility at bioconductor.org.

Dear Anand, On Nov 30, 2011, at 2:04 AM, anand mt [guest] wrote: > > Hi all.. > > i have following questions. > > 1) How many probesets represent a gene on microarray chip ? See manufactures literature for chip. > > 2) How do i access raw intesity value of probes (before > normalization) ? > > 3) Do i need to read cdf file to do that ?? > 2 & 3. Follow the worked examples with affylmGUI, > 4) After pre-processing the data and normalization, we generally go > for significance tests and gene grouping. My question is, if i group > the genes before performing significance test (say now i have 3 > groups based on apoptosis,cell cycle, DNA replication) and then > perform significance test within each group, will the results be > same as that of conventional way ?? Is it a valid method to do so?? > I don't understand this question, but get a list of differentially expressed genes first, The onto-express and pathway-express web sites for which I sent you the links in the course handouts I sent you should enable you to do a good post- gene list analysis. Best wishes, Rich > Sorry if my questions are silly. > > -- output of sessionInfo(): > > --NONE-- > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor ------------------------------------------------------------ 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/ I am a Bayesian. When I see a multiple-choice question on a test and I don't know the answer I say "eeney-meaney-miney-moe". Rose Friedman, Age 14

On Wed, Nov 30, 2011 at 2:04 AM, anand mt [guest] <guest at="" bioconductor.org=""> wrote: > > Hi all.. > > i have following questions. > > 1) How many probesets represent a gene on microarray chip ? > That depends on the array platform. For a given platform, you can use the annotation packages to answer this question. To get started, take a look at: http://bioconductor.org/help/workflows/annotation-data/ > 2) How do i access raw intesity value of probes (before normalization) ? This will depend on the array platform and the software package you are using to do your analysis. Some specifics are probably needed. To get started, be sure to take a look at: http://bioconductor.org/help/workflows/oligo-arrays/ > 3) Do i need to read cdf file to do that ?? Generally not. Depending on the software package that applies, the data from the CDF file are usually repackaged for use in bioconductor. Again, some specifics of your data and experiment are important. > 4) After pre-processing the data and normalization, we generally go for significance tests and gene grouping. My question is, if i group the genes before performing ?significance test (say now i have 3 groups based on apoptosis,cell cycle, DNA replication) and then perform significance test within each group, will the results be same as that of conventional way ?? Is it a valid method to do so?? > You might take a look at this question and response on biostar: http://biostar.stackexchange.com/questions/14796/gene-expression- analysis-microarrays-geneset Hope that helps. Sean > Sorry if my questions are silly. > > ?-- output of sessionInfo(): > > --NONE-- > > -- > Sent via the guest posting facility at bioconductor.org. > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >