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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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