[BioC] ReadAffy can not find function read.AnnotatedDataFrame

[James W. MacDonald]

Hi Georg,

Georg Otto wrote:
> Hi,
> 
> I am having a problem using ReadAffy using the new AnnotatedDataFrame class:
> 
> targets<-new("AnnotatedDataFrame")
> pData(targets)<-read.table("Targets.txt", header=TRUE, row.names=2)
> 
> Data<-ReadAffy(celfile.path =cel.path,
>                filenames = sampleNames(targets),
>                verbose=TRUE)
> 
> Error in AllButCelsForReadAffy(..., filenames = filenames, widget = widget,  : 
> 	could not find function "read.AnnotatedDataFrame"
> 
> I have the newest devel version of Biobase installed (see below)

No, that version of Biobase is 0.0.06 versions old ;-D. The newest 
version is 1.13.19. Using an old version of R and devel versions of BioC 
packages is likely to result in these sorts of problems because you 
cannot easily use biocLite() to update things. I would recommend getting 
the newest version of Biobase, then getting the repos list, and then 
using update packages.

a <- biocReposList()
update.packages(repos=a, ask=FALSE)

I'm not familiar with doing things on MacOS, but on windows adding a 
type="source" will usually work better because the binaries are 
sometimes not built, and usually take longer to propagate anyway. I 
assume you have to be set up to build source packages on MacOS as well?

Also, RSiteSearch() doesn't search the BioC listserv. You have to go to 
the BioC website and click on the 'Join mailing list' link, then the 
link saying something about searchable archives provided by gmane.

Best,

Jim



> 
> RSiteSearch("read.AnnotatedDataFrame")
> 
> did not give me a result.
> 
> Any idea what is wrong here or where I can find the requested function?
> 
> Best,
> 
> Georg
> 
> 
> 
> 
>>sessionInfo()
> 
> R version 2.4.0 (2006-10-03) 
> powerpc-apple-darwin8.7.0 
> 
> locale:
> C
> 
> attached base packages:
> [1] "splines"   "tools"     "stats"     "graphics"  "grDevices" "utils"    
> [7] "datasets"  "methods"   "base"     
> 
> other attached packages:
>      maPlot  maAnalysis      hopach     cluster geneplotter    annotate 
>       "1.0"       "1.0"     "1.8.0"    "1.11.2"    "1.12.0"    "1.13.2" 
>    affydata       limma  simpleaffy  genefilter    survival        affy 
>    "1.10.0"     "2.9.4"     "2.9.0"    "1.13.1"      "2.29"    "1.13.9" 
>      affyio     Biobase 
>     "1.3.1"   "1.13.13"
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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