Dear Sir/madam, I hope that this email finds you well. I am trying to annotate affymetrix data that I downloaded from GEO. I used the following script which I obtained from the annaffy package vignette but it doesn't work. I have copied the script and R responses below. I would really appreciate your help as I am new to bioconductor and have no experience in this field. Here is the script: > library(annaffy) Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: KEGG.db > aaf.handler() [1] "Probe" "Symbol" "Description" [4] "Chromosome" "Chromosome Location" "GenBank" [7] "Gene" "Cytoband" "UniGene" [10] "PubMed" "Gene Ontology" "Pathway" > anncols <- aaf.handler()[c(1:4)] > anntable <- aafTableAnn(probeids[1:150], ?hgu133plus2.db?, Error: unexpected input in "anntable <- aafTableAnn(probeids[1:150], ?" > library(hgu133plus2.db) Loading required package: org.Hs.eg.db > library(hgu133plus2probe) > anntable <- aafTableAnn(probeids[1:150], ?hgu133plus2?, Error: unexpected input in "anntable <- aafTableAnn(probeids[1:150], ?" > aafTable <- aafTableAnn(probeids[1:150], ?hgu133plus2?, Error: unexpected input in "aafTable <- aafTableAnn(probeids[1:150], ?" > aafTable <- aafTableAnn(probeids[1:150], ?hgu133plus2.db?, Error: unexpected input in "aafTable <- aafTableAnn(probeids[1:150], ?" > anncols) I can't get past this but I want to go on and do the following: > saveHTML(anntable, ?ex1.html?, title = ?example table without data?) > testtable <- aafTable(?t-statistic? = topTable[index[1:150]], > signed = TRUE > table <- merge(anntable, testtable) > exportable <- aafTableInt(data, probeids = probeids[1:150]) > table <- merge(table, exportable) > saveHTML(table, ?example2.html?, title = ?Example table with data?) I really hope that you can help me with this. I look forward to hearing from you soon. Best Wishes, Katie

Hi Katie -- On 05/13/2010 05:12 AM, Taylor, Katie wrote: > Dear Sir/madam, > > I hope that this email finds you well. I am trying to annotate affymetrix data that I downloaded from GEO. I used the following script which I obtained from the annaffy package vignette but it doesn't work. I have copied the script and R responses below. I would really appreciate your help as I am new to bioconductor and have no experience in this field. Here is the script: > >> library(annaffy) > Loading required package: GO.db > Loading required package: AnnotationDbi > Loading required package: DBI > Loading required package: KEGG.db >> aaf.handler() > [1] "Probe" "Symbol" "Description" > [4] "Chromosome" "Chromosome Location" "GenBank" > [7] "Gene" "Cytoband" "UniGene" > [10] "PubMed" "Gene Ontology" "Pathway" >> anncols <- aaf.handler()[c(1:4)] >> anntable <- aafTableAnn(probeids[1:150], ?hgu133plus2.db?, > Error: unexpected input in "anntable <- aafTableAnn(probeids[1:150], ?" Probably you are cutting and pasting from some editor into R. Those things that look like quotation marks "hgu133plus2.db" are not, but instead are UTF8-encoded characters > utf8ToInt('?') [1] 8220 > ## expected this... > utf8ToInt('"') [1] 34 You'll want to use an editor that allows you to easily copy / paste 'plain' or 'ascii' text. For instance, on Windows use the editor built in to the R gui (under the File menu, I think). Providing sessionInfo() might help here. Martin >> library(hgu133plus2.db) > Loading required package: org.Hs.eg.db >> library(hgu133plus2probe) >> anntable <- aafTableAnn(probeids[1:150], ?hgu133plus2?, > Error: unexpected input in "anntable <- aafTableAnn(probeids[1:150], ?" >> aafTable <- aafTableAnn(probeids[1:150], ?hgu133plus2?, > Error: unexpected input in "aafTable <- aafTableAnn(probeids[1:150], ?" >> aafTable <- aafTableAnn(probeids[1:150], ?hgu133plus2.db?, > Error: unexpected input in "aafTable <- aafTableAnn(probeids[1:150], ?" >> anncols) > > I can't get past this but I want to go on and do the following: > >> saveHTML(anntable, ?ex1.html?, title = ?example table without data?) >> testtable <- aafTable(?t-statistic? = topTable[index[1:150]], >> signed = TRUE >> table <- merge(anntable, testtable) >> exportable <- aafTableInt(data, probeids = probeids[1:150]) >> table <- merge(table, exportable) >> saveHTML(table, ?example2.html?, title = ?Example table with data?) > > I really hope that you can help me with this. I look forward to hearing from you soon. > > Best Wishes, > > Katie > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor -- Martin Morgan Computational Biology / Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 Location: Arnold Building M1 B861 Phone: (206) 667-2793

Hello, I hope this email finds you well. I am trying to annotate annaffy data and i'm running into some problems. One problem that I faced last week was fixed with your help and I am hoping that you will know what to do with my current problem. I have copied the R output below with the waring messages that I am getting. library(annaffy) Loading required package: GO.db Loading required package: AnnotationDbi Loading required package: DBI Loading required package: KEGG.db > aaf.handler() [1] "Probe" "Symbol" "Description" [4] "Chromosome" "Chromosome Location" "GenBank" [7] "Gene" "Cytoband" "UniGene" [10] "PubMed" "Gene Ontology" "Pathway" > anncols <- aaf.handler()[c(1:4, 7, 10)] > anntable <- aafTableAnn(probeids[1:100], "hgu133plus2.db", + anncols) Loading required package: hgu133plus2.db Loading required package: org.Hs.eg.db Error in probeids[1:100] : object of type 'closure' is not subsettable Error in as.list(probeids) : error in evaluating the argument 'x' in selecting a method for function 'as.list' > anntable <- aafTableAnn(probeids[1:54676], "hgu133plus2.db", + anncols) Error in probeids[1:54676] : object of type 'closure' is not subsettable Error in as.list(probeids) : error in evaluating the argument 'x' in selecting a method for function 'as.list' > I don't know what to do with the probids. Any help that you give me would be greatly appreciated. Best Wishes, Katie