Dear all, This question might sound very naive to most of you but I am new at analyzing affymetrix array data using R/Bioconductor packages. I have two cel files generated from HT430 Mouse genome. I have to find differentially expressed genes in the treated mouse as compared to the control. For this , I downloaded the "affy" package and got the express set (eset) of the differentially expressed genes. I used the rma function to normalization , Background correction and differential expression. Now , I want to annotate these genes and find out there significance in several Pathways. How do I go about doing that?. Also , I read a few topics where they say I need to load the library of annotation (ht430mg here). But where do I get this database?. Any help will be much appreciated as I am new to this topic any sort of guidance will be really helpful. Thanks, Himanshu Sharma. [[alternative HTML version deleted]]

Hi Himansha, I am using GSEA, the java version. I would like to know what other tools are used for pathway anlaysis. Wenhuo On Fri, Apr 13, 2012 at 12:09 PM, <hsharm03@students.poly.edu> wrote: > > Dear all, > This question might sound very naive to most of you but I am new at > analyzing affymetrix array data using R/Bioconductor packages. > I have two cel files generated from HT430 Mouse genome. I have to find > differentially expressed genes in the treated mouse as compared to the > control. > For this , I downloaded the "affy" package and got the express set (eset) > of the differentially expressed genes. I used the rma function to > normalization , Background correction and differential expression. Now , I > want to annotate these genes and find out there significance in several > Pathways. How do I go about doing that?. Also , I read a few topics where > they say I need to load the library of annotation (ht430mg here). But where > do I get this database?. > Any help will be much appreciated as I am new to this topic any sort of > guidance will be really helpful. > Thanks, > Himanshu Sharma. > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Wenhuo Hu Park lab Memorial Sloan Kettering Cancer Center Zuckerman Research Building 408 East 69th Street Room ZRC-527 New York, NY 10065 Phone 646-888-3220 huw@mskcc.org [[alternative HTML version deleted]]

On Fri, 13 Apr 2012 16:09:39 +0000 <hsharm03 at="" students.poly.edu=""> wrote: > > Dear all, > This question might sound very naive to most of you but I am new at > analyzing affymetrix array data using R/Bioconductor packages. > I have two cel files generated from HT430 Mouse genome. I have to > find differentially expressed genes in the treated mouse as compared > to the control. > For this , I downloaded the "affy" package and got the express set > (eset) of the differentially expressed genes. I used the rma function > to normalization , Background correction and differential expression. > Now , I want to annotate these genes and find out there significance > in several Pathways. How do I go about doing that?. Also , I read a > few topics where they say I need to load the library of annotation > (ht430mg here). But where do I get this database?. > Any help will be much appreciated as I am new to this topic any sort > of guidance will be really helpful. > Thanks, > Himanshu Sharma. Hello Himanshu, Check out the workflows at the Bioconductor Web site. Read the manuals of the packages. Run the sample sessions. http://bioconductor.org/help/workflows/ In your case, clicking the Accessing Annotation Data link would help. Regards, Edwin -- > _______________________________________________ > 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 Dr. Edwin Groot AG Laux Institut fuer Biologie III Schaenzlestr. 1 79104 Freiburg, Deutschland +49 761-2032948