search for: hgu133plus2

Hi: I have clustered microarray gene expression data and trying to map between microarray probe, gene, pathway, gene ontology, and homology for a set of (affy) microarray probes. Is there any package in R which facilitates this? I am looking at bioconductor, but till now could not find a solution. A link to some worked example would be appreciated. Thanks and regards. John [[alternative HTML

...k ago the help.search function dies when used in the simple help.search("something") usage. The error is Error in rbind(...) : number of columns of matrices must match (see arg 203) After some effort I have traced it down to the annotation packages. I installed GO, KEGG, mgu74[abc]v2 and hgu133plus2 all version 1.7.0 When I move these out of the library directory, help.search() functions correctly again. I have not tracked it any further -- just wanted to know if anyone else had noticed it. Gerard Tromp

...pData(pd)), phenoData = pd, verbose = TRUE) #### normalize x <- expresso(a, bg.correct = FALSE, normalize.method = "vsn", normalize.param = list(subsample = 1000), pmcorrect.method = "pmonly", summary.method = "medianpolish") ### genes with highest variation library(hgu133plus2.db) rsd <- apply(exprs(x), 1, sd) sel <- order(rsd, decreasing = TRUE)[1:250] u<-mget(row.names(exprs(x)[sel,]),hgu133plus2SYMBOL) heatmap(exprs(x)[sel, ], labRow=u) ### in this case it works to extract the gene symbol ### limma contrasts design <- model.matrix(~ -1+factor(c(1,1,1,2...

...error: w1<-as.list(hgu95av2LOCUSID) w2<-unique(unlist(w1)) set.seed(123) myLL<-sample(w2,100) xx <- GOHyperG(myLL) Error in mget(x, env = GOTERM, ifnotfound = NA) : recursive default argument reference In fact first I tried this function with my locusId ' list (with affymetrix hgu133plus2), but I had the same error... Any help is appreciated Regards, Sabrina Sabrina Carpentier Service Bioinformatique Institut Curie - Bat. Trouillet Rossignol (4e étage) 26 rue d'Ulm - 75248 Paris Cedex 5 - FRANCE Tel : +33 1 42 34 65 21 [[alternative HTML version deleted]]

...fName' > sessionInfo() R version 2.10.0 (2009-10-26) x86_64-apple-darwin9.8.0 locale: [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8 attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] hgu133a2.db_2.3.5 hgu133plus2probe_2.5.0 hgu133plus2.db_2.3.5 org.Hs.eg.db_2.3.6 [5] RSQLite_0.7-3 DBI_0.2-4 hgu133a2probe_2.5.0 AnnotationDbi_1.8.1 [9] hgu133a2cdf_2.5.0 hgu133plus2cdf_2.5.0 simpleaffy_2.22.0 gcrma_2.18.0 [13] genefilter_1.28.2 affy_1.24.2 Biobas...

I have recently upgraded to Ubuntu Gutsy and, for the first time, am using a 64-bit installation. After failing miserably to install R from source, not a problem for me in the past with a 32-bit install, I went the route of using the Debian Etch build. This went smoothly, but I am unable to update my numerous R and BioConductor packages, getting non-zero exit status errors on each package. Is