Hi everyone, I'm new to this mailing list, but I have a few questions which I was hoping perhaps someone might be able to help me with. I'm interested in running a microarray experiment. Specifically, I'm using the Affymetrix Human Exon Array ST1.0 platform to study alternative splicing events in a disease. I have downloaded R for windows (R 2.15.1), and tried to download the Annmap package using the following R script source("http://bioconductor.org/biocLite.R") biocLite("annmap") Following which, I get this error message "Annmap is not available (for R version 2.15.1). There are 2 questions which I have in mind: (1) Which R-packages can I use with R 2.15.1 for the purpose of analyzing (and visualizing) alternative splicing events? (2) What version of R is supported by Annmap? Thank you very much for your kind assistance ((: [[alternative HTML version deleted]]

On Sun, Aug 26, 2012 at 3:48 AM, Jeremy Ng <jeremy.ng.wk1990@gmail.com>wrote: > Hi everyone, > > I'm new to this mailing list, but I have a few questions which I was hoping > perhaps someone might be able to help me with. > > I'm interested in running a microarray experiment. Specifically, I'm using > the Affymetrix Human Exon Array ST1.0 platform to study alternative > splicing events in a disease. I have downloaded R for windows (R 2.15.1), > and tried to download the Annmap package using the following R script > > source("http://bioconductor.org/biocLite.R") > biocLite("annmap") > > Following which, I get this error message > > "Annmap is not available (for R version 2.15.1). > > There are 2 questions which I have in mind: > (1) Which R-packages can I use with R 2.15.1 for the purpose of analyzing > (and visualizing) alternative splicing events? > (2) What version of R is supported by Annmap? > > Hi, Jeremy. Annmap is only available in the development repository. Take a look here for how to use the development version of bioconductor: http://bioconductor.org/developers/useDevel/ Sean [[alternative HTML version deleted]]

I would recommend our open-source software AltAnalyze (http://www.altanalyze.org). Although it also works with junction arrays, conventional arrays and RNA-Seq it was first developed for Affy exon arrays. I think you'll find it to be the easiest and most comprehensive solution. It also includes automated Ontology, transcription factor target and pathway enrichment along with automated pathway visualization. To visualize this data currently, use DomainGraph which is included with AltAnalyze (runs in Cytoscape > see the Cytoscape directory). See the associated tutorial and help for more info. Best, Nathan