Hi Peter,
If I understood what you mean, 
you may want to try

 mget(significant, hgu95av2SYMBOL)

well of course significant is a vector of characters 


Best Regards
Anna

 Anna Freni Sterrantino
Ph.D Student 
Department of Statistics
University of Bologna, Italy
via Belle Arti 41, 40124 BO.




________________________________
Da: Peter Schjerling <Peter@mRNA.dk>
A: bioconductor@stat.math.ethz.ch
Inviato: Giovedì 13 novembre 2008, 15:30:39
Oggetto: [BioC] results.summary does not recognize annotations

Hi,

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:

library(simpleaffy)
library(hgu95av2.db)
library(estrogen)
datadir <- system.file("extdata", package = "estrogen")
setwd(datadir)
pd <- read.AnnotatedDataFrame("estrogen.txt", header = TRUE, sep = "", row.names=1)
raw.data <- ReadAffy(filenames = rownames(pData(pd)), phenoData = pd, verbose=T)
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)
cdfName(raw.data)
cleancdfname(cdfName(raw.data))
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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