[BioC] BioC problem with result.summary in simpleaffy

Marietta Herrmann mariherrmann at gmx.de
Fri Jan 9 16:01:25 CET 2009


I have a problem with result.summary in simpleaffy:

> raw.data <- read.affy("covdesc.txt")
> x.rma<-call.exprs(raw.data, "rma")
Background correcting
Calculating Expression
> pw <- pairwise.comparison(x.rma,"genotype")
> pw.filtered<-pairwise.filter(pw)
> summary<-results.summary(pw.filtered, "mouse4302.db")
Loading required package: AnnotationDbi
Loading required package: DBI
Error in get(paste(cdfname, "SYMBOL", sep = "")) :
 variable "mouse4302.dbSYMBOL" was not found

I also tried:
"mouse4302cdf" which gave the same error


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

When I try to go on despite the error I get the next problem, perhaps as
result of the previous error?!

> write.annotation(file="result_simpleaffy.xls",summary)
Error in as.data.frame.default(x[[i]], optional = TRUE) :
  cannot coerce class "standardGeneric" into a data.frame

Perhaps I just made some stupid mistakes?!

Best regards,
Marietta Herrmann

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