Question: help with annaffy package
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gravatar for Taylor, Katie
9.2 years ago by
Taylor, Katie90 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], ?" > 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
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ADD COMMENTlink modified 9.2 years ago • written 9.2 years ago by Taylor, Katie90
Answer: help with annaffy package
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gravatar for Martin Morgan
9.2 years ago by
Martin Morgan ♦♦ 23k
United States
Martin Morgan ♦♦ 23k wrote:
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
ADD COMMENTlink written 9.2 years ago by Martin Morgan ♦♦ 23k
Answer: help with annaffy package
0
gravatar for Taylor, Katie
9.2 years ago by
Taylor, Katie90 wrote:
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
ADD COMMENTlink written 9.2 years ago by Taylor, Katie90
On Mon, May 17, 2010 at 4:45 AM, Taylor, Katie <kt70@leicester.ac.uk> wrote: > 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. > > Hi, Katie. You'll need to provide the code that produced probeids or at least some information about what is in probeids (summary(probeids), head(probeids), class(probeids), as examples). Also, you absolutely need to include sessionInfo() for every email to the list for your question to be adequately answered. Sean [[alternative HTML version deleted]]
ADD REPLYlink written 9.2 years ago by Sean Davis21k
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