[BioC] justRMA couldn't obtain CDF environment

[cstrato]

Dear Jim and Li,

It seems that OncoScan arrays are Genotyping arrays and not expression 
arrays, see:
http://www.affymetrix.com/estore/promotions/mip/index.affx

Package xps can only handle expression arrays and thus does not work 
with OncoScan arrays, but maybe package oligo is able to handle these 
arrays.

Best regards,
Christian


On 6/26/14 8:49 PM, James W. MacDonald wrote:
> 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
>>
>>     [[alternative HTML version deleted]]
>>
>>
>>
>> _______________________________________________
>> Bioconductor mailing list
>> Bioconductor at r-project.org
>> https://stat.ethz.ch/mailman/listinfo/bioconductor
>> Search the archives:
>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>
>