[BioC] help with annaffy package

[Martin Morgan]

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
> 
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-- 
Martin Morgan
Computational Biology / Fred Hutchinson Cancer Research Center
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