Dear members,

I tried to read a batch of Affymetrix *.cel files and perform normalization using 'justRMA', but I got the following error:

Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain OncoScan
Library - package oncoscancdf not installed
Bioconductor - oncoscancdf not available


I couldn't find the package 'oncoscancdf' in Bioconductor.

However, when I used the same code run my old '*.cel' files it worked well. Are there anybody who have the experience about this?

Many thanks,

Li


Here are the codes I run and the output:

> library(affy)
> setwd('U:/li/BR10microarray/data/cel')
> eset=justRMA(filenames=list.celfiles(), normalize=T)
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain OncoScan
Library - package oncoscancdf not installed
Bioconductor - oncoscancdf not available


> source("http://bioconductor.org/biocLite.R")
Bioconductor version 2.14 (BiocInstaller 1.14.2), ?biocLite for help
> biocLite('oncoscancdf')
BioC_mirror: http://bioconductor.org
Using Bioconductor version 2.14 (BiocInstaller 1.14.2), R version 3.1.0.
Installing package(s) 'oncoscancdf'
Warning message:
package ‘oncoscancdf’ is not available (for R version 3.1.0) 

> sessionInfo()
R version 3.1.0 (2014-04-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] affy_1.42.3          Biobase_2.24.0       BiocGenerics_0.10.0  BiocInstaller_1.14.2

loaded via a namespace (and not attached):
[1] affyio_1.32.0         preprocessCore_1.26.1 tools_3.1.0           zlibbioc_1.10.0      
 		 	   		  
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