Question: Processing array with R
0
gravatar for Charlie
22 months ago by
Charlie0
Taiwan
Charlie0 wrote:

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

cdf affy software error R • 527 views
ADD COMMENTlink modified 22 months ago by James W. MacDonald51k • written 22 months ago by Charlie0
Answer: Processing array with R
0
gravatar for James W. MacDonald
22 months ago by
United States
James W. MacDonald51k wrote:

Use oligo, not affy.

library(oligo)
dat <- read.celfiles(list.celfiles())
eset <- rma(dat)
ADD COMMENTlink written 22 months ago by James W. MacDonald51k

Thank you! Seems works!

ADD REPLYlink written 22 months ago by Charlie0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 286 users visited in the last hour