[BioC] hgu133a and gnGNF1Ba

[Cei Abreu-Goodger]

Hi Robert,

The GNF atlas used a custom affy chip for mouse, and for human they used 
hgu133a chips in addition to another custom chip. I have made CDF and 
probe packages for both custom chips, which you can download from:

ftp://ftp.sanger.ac.uk/pub/cei/gngnf1_R_packages.tar.gz

Cheers,

Cei


Robert Castelo wrote:
> hi,
>
> i've downloaded the gene expression atlas data for human and mouse from
> GEO
>
> wget
> ftp://ftp.ncbi.nih.gov/pub/geo/DATA/supplementary/series/GSE1133/GSE1133_RAW.tar
>
> which as far as i know comes from the Affymetrix microarray chips
> hgu133a.
>
> i want to load and process myself these data using RMA in bioconductor.
> after putting the files in the proper directory structure i do the
> following:
>
> library(affy)
> library(hgu133a)
>
> data <- ReadAffy()
> eset <- rma(data)
> Error in getCdfInfo(object) : Could not obtain CDF environment, problems
> encountered:
> Specified environment does not contain gnGNF1Ba
> Library - package gngnf1bacdf not installed
> Data for package affy did not contain gngnf1bacdf
> Bioconductor - gngnf1bacdf not available
>
> and i get the problem above, i'm missing a CDF package called
> gngnf1bacdf. in fact this is the annotation that seems to be attached to
> the .CEL files
>
> annotation(data)
> [1] "gngnf1ba"
> print(data at cdfName)
> [1] "gnGNF1Ba"
>
> so i tried to download it from the bioconductor site:
>
> source("http://www.bioconductor.org/getBioC.R")
> getBioC(c("gngnf1bacdf"))
> Running biocinstall version 2.0.8 with R version 2.5.0 
> Your version of R requires version 2.0 of Bioconductor.
> Warning in install.packages(pkgs = pkgs, repos = repos, dependencies =
> dependencies,  : 
>          argument 'lib' is missing: using '/home/robert/myRlibrary/'
> Warning message:
> package 'gngnf1bacdf' is not available in: install.packages(pkgs = pkgs,
> repos = repos, dependencies = dependencies,  
>
> but as you can see it does not seem to be available. does anyone know
> where can i get this environment CDF package?
>
> this is may sessionInfo():
>
> R version 2.5.0 (2007-04-23) 
> x86_64-unknown-linux-gnu 
>
> locale:
> C
>
> attached base packages:
> [1] "tools"     "stats"     "graphics"  "grDevices" "utils"
> "datasets" 
> [7] "methods"   "base"     
>
> other attached packages:
>       affy    Biobase hgu133acdf    hgu133a     affyio 
>   "1.14.0"   "1.14.0"   "1.16.0"   "1.16.0"    "1.4.0" 
>
>
> thanks!!
> robert.
>
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