mas5 normalization error: unable to find an inherited method for function

Question

Goal: mas5 normalize data.

Problem: when I try the following R code, I get this

error: unable to find an inherited method for function bg.correct for signature ExpressionFeatureSet, character

I have looked on SO, and found the following: What does this mean: unable to find an inherited method for function ‘A’ for signature ‘"B"’, but I am not exactly sure how to fix my specific problem and use the mas5 function properly. I have also looked at this affy manual but still stuck...

installpkg("affy")
library('affy')
setwd("/Users/er/Desktop/DesktopFolders/DataSets/CD8Helios/Microarray/CELfiles/CEL")
cel_Files <- list.celfiles()
affyRaw <- read.celfiles(cel_Files)
eset <- mas5(affyRaw) 

Answer 1

If you are sure that the .cel files were created based on experiments performed on the type of array that works with affy package than you should try this workflow using ReadAffy from affy package.

cel_Files <- list.celfiles()
affyRaw <- affy::ReadAffy(filenames=cel_Files)
eset <- mas5(affyRaw) 

However, it might be the case that the affy package is not designed for your array type. Then, you should switch to the oligo and oligoClasses packages and normalize with analogous function rma

 cel_Files <-  oligoClasses::list.celfiles()
 affyRaw <- oligo::read.celfiles(cel_Files)
 eset <- oligo::rma(affyRaw)