Dear all,

after reading CEL files with affy package's readAffy() function, I try to normalize the data using rmaplus() function from package RefPlus.

I get

Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain RTA-1_0 Library - package rta10cdf not installed Bioconductor - rta10cdf not available

and indeed, the object says

> str(Data)
Formal class 'AffyBatch' [package "affy"] with 10 slots
  ..@ cdfName          : chr "RTA-1_0"

Unfortunately, I cannot find some "rta10cdf" package on BioC. Any ideas?

Best wishes,

Marianna

I don't know the package RefPlus, but based on the error it apparently uses the function ReadAffy() from the library affy to read the CEL files. Problem is that these newest type of arrays are not supported by affy nor a CDF is available; it is recommended to rather use the library oligo (link) to read and process them. To use oligo you will also need the corresponding PdInfo package that can be found here. How to incorporate this with the RefPlus package I don't know.

FWIW: To get a quick start you may want to have a look at the thread Pre-processing of HTA 2.0 array on the analysis of the human variant of this array; the code is easily adaptable to the rat array. It consists of normalization (RMA) and annotation (that can be done on 2 levels, i.e. on the level of probesets or transcripts).