Question: CDF not found
gravatar for ijvechetti
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
ADD COMMENTlink modified 9 weeks ago by Guido Hooiveld2.5k • written 9 weeks ago by ijvechetti0
Answer: CDF not found
gravatar for Guido Hooiveld
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).

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by Guido Hooiveld2.5k

Thank you for your help and for your time. That is what I ended up doing, based on some threads I saw. Thank you for the codes.

ADD REPLYlink written 9 weeks ago by ijvechetti0
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