[BioC] Problem with Annotation of Mouse4302.db in simpleaffy

Marietta Herrmann mariherrmann at gmx.de
Wed Jan 28 18:38:50 CET 2009


I asked this question some weeks ago, but I couldn't solve the problem yet.
I would be very glad if somebody could help me..

I tried to use pairwise.comparison in simpleaffy to get a table of results,
but there is an error with the annotation...

Thanks for your help,

Marietta Herrmann

> data<-ReadAffy()
> pData<-data.frame(genotype=c(1,1,1,2,2,2), replicate=c(1,2,3,1,2,3))
> rownames(pData)<-sampleNames(data)
> vl<-data.frame(c("1 is B6, 2 is D2", "arbitrary numbering"))
> phenoData(data)<-new("AnnotatedDataFrame", data=pData, varMetadata=vl)
> library(gcrma)
> eset<-gcrma(data)
> library(simpleaffy)
> results <- pairwise.comparison(eset, "genotype", spots=data)
> significant<-pairwise.filter(results, fc=log2(2), tt=0.05, present.by.group=T)
[1] "Checking member 1 in group: ' genotype '"
[1] "Checking member 2 in group: ' genotype '"

> summary <- results.summary(significant, "mouse4302")
Error in library(cdfname, character.only = TRUE) :
  there is no package called 'mouse4302'

> summary <- results.summary(significant, "mouse4302.db")
Loading required package: AnnotationDbi
Loading required package: DBI
Error in get(paste(cdfname, "SYMBOL", sep = "")) :
  variable "mouse4302.dbSYMBOL" was not found

> sessionInfo()
R version 2.8.0 (2008-10-20)


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

other attached packages:
 [1] mouse4302.db_2.2.5   RSQLite_0.7-1        DBI_0.2-4
 [4] AnnotationDbi_1.4.1  simpleaffy_2.18.0    genefilter_1.22.0
 [7] survival_2.34-1      mouse4302probe_2.3.0 mouse4302cdf_2.3.0
[10] gcrma_2.14.1         matchprobes_1.14.0   affy_1.20.0
[13] Biobase_2.2.1 

loaded via a namespace (and not attached):
[1] affyio_1.10.1        annotate_1.20.1      preprocessCore_1.4.0

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