[BioC] results.summary does not recognize annotations

Peter Schjerling Peter at mRNA.dk
Thu Nov 13 15:30:39 CET 2008


I have a problem with getting results.summary to recognize the 
annotation files.

If I write:
 > summary <- results.summary(significant, "hgu95av2")
I get:
 > Error in library(cdfname, character.only = TRUE) :
    there is no package called 'hgu95av2'

I have loaded the library (hgu95av2.db) and if I for instance write:
 > mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" )))
I get the correct annotation "TIE1".

I have made a simple test script which result in the error above:

datadir <- system.file("extdata", package = "estrogen")
pd <- read.AnnotatedDataFrame("estrogen.txt", header = TRUE, sep = 
"", row.names=1)
raw.data <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, 
x.mas5 <- call.exprs(raw.data,"mas5")
results <- pairwise.comparison(x.mas5, "estrogen", spots=raw.data)
significant <- pairwise.filter(results, min.exp=log2(100), 
min.exp.no=4, min.present.no=4, present.by.group=T, fc=log2(1.3), tt=0.05)
mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="" )))
summary <- results.summary(significant, "hgu95av2")

I guess it have something to do with the new ".db" format as it used 
to work with an older version of R and Bioconductor. The version I 
use now is R 2.8.0 and updated Bioconductor libraries.

Am I just making some stupid error here as I have been unable to find 
any references to similar problems on the net?

Best regards,
Peter Schjerling

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