[BioC] justRMA couldn't obtain CDF environment

[James W. MacDonald]

Hi Li,

The affy/makecdfenv pipeline is only intended for use with the 3'-bias 
expression arrays. The OncoScan arrays are completely different, and 
won't work with these packages.

I don't know if xps or oligo will work with these arrays either; I don't 
know much about them. However, Affymetrix has their own OncoScan Nexus 
Express Software that you could use.

Best,

Jim



On 6/26/2014 2:22 PM, Li Liu wrote:
> 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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>
>
>
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-- 
James W. MacDonald, M.S.
Biostatistician
University of Washington
Environmental and Occupational Health Sciences
4225 Roosevelt Way NE, # 100
Seattle WA 98105-6099