0
9 weeks ago by
ijvechetti0 wrote:

Hello, I'm having a problem with Affymetrix array for Clariom S Rat

When i run I get the follow error:

library(affy) data <- ReadAffy() eset <- affy::rma(data)

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

I have tried to install clariomsrattranscriptcluster.db pd.clariom.s.rat

But still not working, what could I do?

microarray affy • 122 views
modified 9 weeks ago by Guido Hooiveld2.5k • written 9 weeks ago by ijvechetti0
1
9 weeks ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

The Affymetrix Clariom S Rat arrays are so-called 3rd generation expression arrays, and the analysis of these type of arrays is NOT possible anymore with the library affy (see e.g. here). In contrast, you should use the library oligo (here) + the corresponding PdInfo (platform design info) library (here) to process these arrays.

Some code to get you started can be found here. Note1: please read that complete thread! Note2: When using that code, you obviously have to change the name of the respective libraries to the rat variant (from human).