[BioC] results.summary does not recognize annotations

[Jenny Drnevich]

HI Peter,

Like Jim, I thought you should just try:

 > summary <- results.summary(significant, "hgu95av2.db")

But thanks to your reproducible example I got the following error:

Error in get(paste(cdfname, "SYMBOL", sep = "")) :
   variable "hgu95av2.dbSYMBOL" was not found

So it does look like there is an error somewhere in the 
results.summary code - it now needs to strip off the .db from the 
cdfname before pasting on "SYMBOL" etc.


HTH,
Jenny

At 08:30 AM 11/13/2008, 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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Jenny Drnevich, Ph.D.

Functional Genomics Bioinformatics Specialist
W.M. Keck Center for Comparative and Functional Genomics
Roy J. Carver Biotechnology Center
University of Illinois, Urbana-Champaign

330 ERML
1201 W. Gregory Dr.
Urbana, IL 61801
USA

ph: 217-244-7355
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e-mail: drnevich at illinois.edu