Dear Steve, Sorry, I am referring to this part which was there in GOstats documentation, for data(ALL) 2.1 Non-speci c ltering First we load the ALL data object and extract the subset of the data we wish to analyze: subjects with either no cytogenetic abnormality (\NEG") or those with "ALL1/AF4". > data(ALL, package = "ALL") > subsetType <- "ALL1/AF4" > Bcell <- grep("^B", as.character(ALL$BT)) > bcrAblOrNegIdx <- which(as.character(ALL$mol) %in% c("NEG", subsetType)) > bcrAblOrNeg <- ALL[, intersect(Bcell, bcrAblOrNegIdx)] > bcrAblOrNeg$mol.biol = factor(bcrAblOrNeg$mol.biol) We begin our non-speci c ltering by removing probe sets that have no Entrez Gene iden- ti er in our annotation data. > entrezIds <- mget(featureNames(bcrAblOrNeg), envir = hgu95av2ENTREZID) > haveEntrezId <- names(entrezIds)[sapply(entrezIds, function(x) !is.na(x))] > numNoEntrezId <- length(featureNames(bcrAblOrNeg)) - length(haveEntrezId) > bcrAblOrNeg <- bcrAblOrNeg[haveEntrezId, ] Could you please tell me how to follow here for my data.,.....Thanks in advance. ----- Original Message ----- From: Steve Lianoglou <mailinglist.honeypot@gmail.com> Date: Monday, November 8, 2010 6:55 pm Subject: Re: [BioC] Can any one please help me regadrding Illumina humanv3.microarray To: Pradeep Battula <prabat at="" utu.fi=""> Cc: bioconductor at stat.math.ethz.ch > Hi Pradeep, > > (Please keep all correspondence on list by using "reply-all" when > replying to bioc-help messages) > > On Mon, Nov 8, 2010 at 11:38 AM, Pradeep Battula <prabat at="" utu.fi=""> wrote: > > Dear Steve, > > > > Thanks a lot for your suggestion. and I also want to know, whether I > have to perform all those Non-specific filtering tests, for the gene > universe....Thanks in advance. > > I'm sorry, I don't follow ... what non-specific filtering tests to the > gene universe are you referring to? > > -steve > > > > > Regards, > > Pradee. > > > > ----- Original Message ----- > > From: Steve Lianoglou <mailinglist.honeypot at="" gmail.com=""> > > Date: Monday, November 8, 2010 5:55 pm > > Subject: Re: [BioC] Can any one please help me regadrding Illumina humanv3.microarray > > To: Pradeep Battula <prabat at="" utu.fi=""> > > Cc: bioconductor at stat.math.ethz.ch > > > > > >> Hi, > >> > >> On Mon, Nov 8, 2010 at 10:44 AM, Pradeep Battula <prabat at="" utu.fi=""> wrote: > >> > Dear All, > >> > > >> > I want to write a function that performs hypergeometric test for > >> over representation against GO and KEGG, for the available example > of > >> data of > >> > background.Datat: Entrez identifiers of all probes present on > >> Illumina human HT12 v3. microarray > >> > DEgenes.Data: Differentially expressed genes in a real study carried > >> out on Illumina HT12 v3. microarray > >> > > >> > But, the relevant documentation provided in "GOstats" and "topGO" > >> are explained using a microarray data set ?from a clinical trial in > >> acute lymphoblastic leukemia (ALL). > >> > > >> > Now I want to know, can I apply the same documentation to my > >> available data or there any minor changes I have to make. > >> > >> If both your background.Data and DEgenes.Data are simply vectors of > >> entrez id's, then this is pretty straightforward. With GOstats, you > >> can do: > >> > >> R> ? params <- new("GOHyperGParams", geneIds=DEgenes.data, > >> ? ? ? ? ? ? ? ? universeGeneIds=background.Data, annotation='org.Hs.eg.db', > >> ? ? ? ? ? ? ? ? ontology='BP', ...) > >> R> go.bp <- hyperGTest(params) > >> > >> -steve > >> > >> -- > >> 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 > > > > > > -- > 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