Question: Cdf file problem
0
gravatar for sam.neaves
4.0 years ago by
sam.neaves20
United Kingdom
sam.neaves20 wrote:

I am trying to make a csv file to do some machine learning in WEKA, the data set I want to use is GSE31799. I have used the following lines of code with other data sets with out a problem (For example GSE2109).

I have downloaded the .CEL files into a folder extracted them and created a phenodata file. 

celfiles <- read.affy(covdesc="phenodata.txt")
celfiles.gcrma <-gcrma(celfiles)
eset<-exprs(celfiles.gcrma)
Transposed <- t(eset)
write.csv(Transposed, file="GSE31799_gcrma.csv", append= FALSE, row.names=TRUE, col.names=TRUE)

However I get the following error when executing the second line: 

Warning: unable to access index for repository http://brainarray.mbni.med.umich.edu/bioc/bin/windows/contrib/2.15
Error in getCdfInfo(object) : 
  Could not obtain CDF environment, problems encountered:
Specified environment does not contain RM-HU01Aa520485
Library - package rmhu01aa520485cdf not installed
Bioconductor - rmhu01aa520485cdf not available

I think I have a cdf file that goes with this data set (rmhu01aa520485.cdf) 

But i can't work out how to use it? 

 

 

 

microarray cdf R • 1.9k views
ADD COMMENTlink modified 2.4 years ago by fengshugluck0 • written 4.0 years ago by sam.neaves20
0
gravatar for fengshugluck
2.4 years ago by
fengshugluck0 wrote:

Hi Dear, Have you settled the problem already?

I encountered the same problem like yours recently.I could download a cdf file from GEO, but R showed "could not obtain CDF environment". I don't know how to solve it either.

So if you have got the answer,could you please send me an Email to help me? I will appreciate it very much.

ADD COMMENTlink written 2.4 years ago by fengshugluck0
0
gravatar for fengshugluck
2.4 years ago by
fengshugluck0 wrote:

My Email is fengshugluck@gmail.com. Thanks a lot!

ADD COMMENTlink written 2.4 years ago by fengshugluck0
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