[BioC] help with annaffy package

[Taylor, Katie]

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