Hello everyone:
I am a new research assistant in bioinformatics field in Taiwan.
Recently, I am processing a data with 12 gene expression samples of Affymetrics.
But when I used R to run analysis it showed following messages:
library(affy)
file=ReadAffy()
file
AffyBatch object
size of arrays=548x548 features (20 kb)
cdf=Clariom_S_Mouse (??? affyids)
number of samples=12
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain Clariom_S_Mouse
Library - package clariomsmousecdf not installed
Bioconductor - clariomsmousecdf not available
In addition: Warning message:
missing cdf environment! in show(AffyBatch)
I search the clariomsmousecdf in Bioconductor website (http://www.bioconductor.org/packages/release/data/annotation/)
But there is only two similar files:
clariomsmousetranscriptcluster.db
clariomsmousehttranscriptcluster.db
Does this means there is not CDF file provided in Bioconductor website?
Later, I try to normalized my data by this way:
eset<-affy::rma(file)
But it still showed
Error in getCdfInfo(object) :
Could not obtain CDF environment, problems encountered:
Specified environment does not contain Clariom_S_Mouse
Library - package clariomsmousecdf not installed
Bioconductor - clariomsmousecdf not available
Seems clariomsmousecdf is a key package, but I can't find it.
Can anyone help me with this problem?
Thanks a lot!
Charlie
Thank you! Seems works!