[BioC] results.summary function returns error

[Julia Jacobson [guest]]

Hello everybody out there using the simpleaffy Bioconductor package,

In order to get started with microarray analysis, I'm trying to reproduce the steps in the Vignette of the simpleaffy package.
I downloaded the sample CEL files from the homepage of the bioinformatics group of the university of Manchester (http://bioinformatics.picr.man.ac.uk/experiments/amplification/CEL/) and performed the following steps:

R> library(simpleaffy)
R> x <- read.affy("covdesc")
R> x.rma <- call.exprs(x,"rma")
R> pw <- pairwise.comparison(x.rma,"rna",c("10ng","100ng"))
R> pw.filtered <- pairwise.filter(pw)
R> library("hgu133a.db")

So far, so good. The following command yields the error message:

R> summary <- results.summary(pw.filtered,"hgu133a.db")
Error is get(paste(cdfname, "SYMBOL", sep = "")) : 
  Object "hgu133a.dbSymbol" not found

I've done extensive web search and found out there's been a migration of the annotation data to SQLite format. This seems to cause problems concerning the annotation carried out by the "results.summary" function.
In the thread https://stat.ethz.ch/pipermail/bioconductor/2009-January/025787.html is mentioning a very similar problem I have and solves this thread by redefining the "get.annotation" function

get.annotation <- function (x, cdfname, verbose = FALSE) {
     library(cdfname, character.only = TRUE)
     cdfname <- sub("\\.db$", "", cdfname)  ## add this line
}

I tried this to no success.
Moreover, I entered the following commands, but also got errors:


R> summary <- results.summary(pw.filtered,hgu133a.db)
R> summary <- results.summary(pw.filtered,"hgu133a")
R> summary <- results.summary(pw.filtered,hgu133a)

What additional diagnostics could I run to pin down the problem?

Kind regards,
Julia

 -- output of sessionInfo(): 

R version 2.14.1 (2011-12-22)
Platform: i686-pc-linux-gnu (32-bit)

locale:
 [1] LC_CTYPE=de_DE.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=de_DE.UTF-8        LC_COLLATE=de_DE.UTF-8    
 [5] LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=de_DE.UTF-8   
 [7] LC_PAPER=C                 LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=de_DE.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] hgu133a.db_2.6.3      org.Hs.eg.db_2.6.4    RSQLite_0.11.2       
 [4] DBI_0.2-5             hgu133acdf_2.9.1      AnnotationDbi_1.16.19
 [7] simpleaffy_2.30.0     gcrma_2.26.0          genefilter_1.36.0    
[10] affy_1.32.1           Biobase_2.14.0       

loaded via a namespace (and not attached):
 [1] affyio_1.22.0         annotate_1.32.3       BiocInstaller_1.2.1  
 [4] Biostrings_2.22.0     IRanges_1.12.6        preprocessCore_1.16.0
 [7] splines_2.14.1        survival_2.36-10      tools_2.14.1         
[10] xtable_1.7-0          zlibbioc_1.0.1       

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