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

Use oligo, not affy.

library(oligo)
dat <- read.celfiles(list.celfiles())
eset <- rma(dat)