[BioC] results.summary does not recognize annotations

[James W. MacDonald]

Hi Peter,

Have you tried

results.summary(significant, "hgu95av2.db") ?

Best,

Jim



Peter Schjerling wrote:
> 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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-- 
James W. MacDonald, M.S.
Biostatistician
Hildebrandt Lab
8220D MSRB III
1150 W. Medical Center Drive
Ann Arbor MI 48109-0646
734-936-8662