Entering edit mode
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/GSE11
33_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.
