Hi All, I have a list of clusters generated through biolayout which I need to annotate for GO annotations. I can do this one-by-one using DAVID etc but as there are 97 clusters this is a rather lengthy procedure. Do any of you know of any tools were you can upload multiple lists of genes to be annotated for go over-representation (or failing that pathway enrichment)? Any help would be greatly appreciated, Helen -----Original Message----- From: bioconductor-bounces@r-project.org [mailto:bioconductor- bounces@r-project.org] On Behalf Of James W. MacDonald Sent: 28 October 2013 13:50 To: DR DHANJIT KUMAR DAS [guest] Cc: bioconductor at r-project.org; dasdjk at gmail.com Subject: Re: [BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment You should be using either the oligo or xps package for this array. For oligo, you need the pdInfoBuilder package, and some files from Affymetrix. You need the pgf, clf and mps files that are in this zipfile: http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/MarGene- 1_0-st_rev01/MarGene-1_0-st_rev01.zip And you need the probeset csv file http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2 /MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv.zip and the transcript csv file http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2 /MarGene-1_0-st-v1.na33.2.caljac3.transcript.csv.zip and then you can make the pd.margene.1.0.st.v1 package following these instructions: https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html after which you can install using install.packages("pd.margene.1.0.st.v1/", repos=NULL, type="source") If you want to use xps there are a set of vignettes here: http://www.bioconductor.org/packages/release/bioc/html/xps.html and Christian Stratowa is very helpful, so you can ask questions here if you get stuck. Best, Jim On Monday, October 28, 2013 6:12:15 AM, DR DHANJIT KUMAR DAS [guest] wrote: > > I would like to analyze data using Marmoset Gene 1.0 ST Array. While reading the CEL file into R environment, error message is showing as "Library - package margene10stcdf not installed" > > How to install the package MarGene-1_0st package into R environment? The R script is attached for your reference. > > The part No of the array is 901961. > > -- output of sessionInfo(): > >> library(affy) >> eset.rma <- justRMA(celfile.path="C:/Dhanjit/Marmoset-Dr Uddhav/CEL >> FILE/") > Error in getCdfInfo(object) : > Could not obtain CDF environment, problems encountered: > Specified environment does not contain MarGene-1_0-st Library - > package margene10stcdf not installed Bioconductor - margene10stcdf not > available > > > -- > 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 -- James W. MacDonald, M.S. Biostatistician University of Washington Environmental and Occupational Health Sciences 4225 Roosevelt Way NE, # 100 Seattle WA 98105-6099 _______________________________________________ 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

Hello Helen, If you can carry out one GO enrichment analysis in R, you can carry out 97 almost equally well. You just have to have a script for doing it once. Then you generate a list of you gene sets. And then you can use R: lapply on the list. the syntax is: listofresultmatrices <- lapply(listofgenesets, function(s) { your entire script for doing analysis on one genelist }) You script should produce a matrix as an output and you would have a list of 97 results matrices. You can then script some sort of a summarization function. I have done this for topGO analysis: you can search "label:bioconductor topGO Pekka". It uses lists as gene symbols, a vector of ensembl gene ids for the background and GO "Biological Process" categories. TopGO is a nice package because it avoids the problem of GO-enrichment (and all hypergeometric enrichment analysis) that you always get the least informative largest genesets as the top-results. Probably because the method does not properly take into account inter-gene correlations and does not weight results according to significance of differential expression (how could it since it only has information on gene names). Best, Pekka 2013/10/28 Helen Smith <helen.smith-2 at="" manchester.ac.uk="">: > Hi All, > > I have a list of clusters generated through biolayout which I need to annotate for GO annotations. I can do this one-by-one using DAVID etc but as there are 97 clusters this is a rather lengthy procedure. > Do any of you know of any tools were you can upload multiple lists of genes to be annotated for go over-representation (or failing that pathway enrichment)? > > Any help would be greatly appreciated, > Helen > > -----Original Message----- > From: bioconductor-bounces at r-project.org [mailto:bioconductor- bounces at r-project.org] On Behalf Of James W. MacDonald > Sent: 28 October 2013 13:50 > To: DR DHANJIT KUMAR DAS [guest] > Cc: bioconductor at r-project.org; dasdjk at gmail.com > Subject: Re: [BioC] Installing library package (Marmoset Gene 1.0 ST Array) into R environment > > You should be using either the oligo or xps package for this array. For oligo, you need the pdInfoBuilder package, and some files from Affymetrix. > > You need the pgf, clf and mps files that are in this zipfile: > > http://www.affymetrix.com/Auth/analysis/downloads/lf/wt/MarGene- 1_0-st_rev01/MarGene-1_0-st_rev01.zip > > And you need the probeset csv file > > http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2 /MarGene-1_0-st-v1.na33.2.caljac3.probeset.csv.zip > > and the transcript csv file > > http://www.affymetrix.com/Auth/analysis/downloads/na33/wtgene-32_2 /MarGene-1_0-st-v1.na33.2.caljac3.transcript.csv.zip > > and then you can make the pd.margene.1.0.st.v1 package following these > instructions: > > https://stat.ethz.ch/pipermail/bioconductor/2013-March/051335.html > > after which you can install using > > install.packages("pd.margene.1.0.st.v1/", repos=NULL, type="source") > > If you want to use xps there are a set of vignettes here: > > http://www.bioconductor.org/packages/release/bioc/html/xps.html > > and Christian Stratowa is very helpful, so you can ask questions here if you get stuck. > > Best, > > Jim > > > > > On Monday, October 28, 2013 6:12:15 AM, DR DHANJIT KUMAR DAS [guest] > wrote: >> >> I would like to analyze data using Marmoset Gene 1.0 ST Array. While reading the CEL file into R environment, error message is showing as "Library - package margene10stcdf not installed" >> >> How to install the package MarGene-1_0st package into R environment? The R script is attached for your reference. >> >> The part No of the array is 901961. >> >> -- output of sessionInfo(): >> >>> library(affy) >>> eset.rma <- justRMA(celfile.path="C:/Dhanjit/Marmoset-Dr Uddhav/CEL >>> FILE/") >> Error in getCdfInfo(object) : >> Could not obtain CDF environment, problems encountered: >> Specified environment does not contain MarGene-1_0-st Library - >> package margene10stcdf not installed Bioconductor - margene10stcdf not >> available >> >> >> -- >> 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 > > -- > James W. MacDonald, M.S. > Biostatistician > University of Washington > Environmental and Occupational Health Sciences > 4225 Roosevelt Way NE, # 100 > Seattle WA 98105-6099 > > _______________________________________________ > 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 > > _______________________________________________ > 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