Question: run affy package encounts clariomdhumancdf error
0
8 months ago by
833101990
833101990 wrote:

Hello everyone! I'm going to analyses the CEL files for genes expression information. Run the commands as the affy package's guide pdf provided, some error occurred below:

library(affy) setwd('D://R/affy/') Data <- ReadAffy() eset <- rma(Data)

##### >eset <- rma(Data)

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

I tried to install the 'ClariomDHuman' package:

library(BiocInstaller) BiocManager::install("ClariomDHuman")

continue to run: eset <- rma(Data)

eset <- rma(Data) Error in getCdfInfo(object) : Could not obtain CDF environment, problems encountered: Specified environment does not contain ClariomDHuman Library - package clariomdhumancdf not installed Bioconductor - clariomdhumancdf not available

What can i do to fix this bug？ I'm new to R that I haven't mastered many concepts yet. It would be great if you could give detailed steps and specific guidance. Thank you for your guidance and advice, which will help me get started in the R field.

modified 8 months ago by Guido Hooiveld2.5k • written 8 months ago by 833101990
Answer: run affy package encounts clariomdhumancdf error
3
8 months ago by
Guido Hooiveld2.5k
Wageningen University, Wageningen, the Netherlands
Guido Hooiveld2.5k wrote:

As said in the related thread started by you, and that now is deleted (also by you?!), these are 3rd generation Affymetrix arrays for which NO Chip Definition File (CDF) is available. As a result, these arrays can NOT be analyzed using the library affy, but rather should be analyzed using oligo and the corresponding PdInfo package. Some code to get you started + some relevant links were already provided in the deleted thread....