Cdf file problem

Question

[sam.neaves]

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?

Answer 1

[fengshugluck]

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.

Answer 2

[fengshugluck]

My Email is [e-mail]. Thanks a lot!