Hi everybody,

I have an old problem that i put aside at each time. I search but i never found a valid reponse for me.  My script to normalize array data use the affy package but it only work with the 2.15 version of R. When i use it with version 3.x it always display the same error above: 

Erreur : 

The affy package is not designed for this array type.
Please use either the oligo or xps package.

So why the affy package did not run with new versions of R and why it tell me that it is array type problem ? I only use the list.celfile() and ReadAffy() functions. I think i missed something ?

More the affy package seems to still work because it is still mention in the updated limma  userguide for analyzing single channel affymetrix array.

More the 2.15 version of R dont work with new versions of MacOS so impossible to use my script with macOS.

Thank you for your answers!

The answer is in the error message. You have to use either oligo or xps to analyze those arrays. So change your scripts to use one of those packages.

ok you are right i will do that. thank you !

Just to know, do you know why it is impossible to use the ReadAffy function in the affy package with version 3.x ?

I tied the oligo package but i did not come to use the rma function because i can't create a readaffy batch object without the affy package and i try xps but i did not come to install the package, i had this error: 

Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  impossible de charger l'objet partagé '/Library/Frameworks/R.framework/Versions/3.2/Resources/library/xps/libs/xps.so':
  dlopen(/Library/Frameworks/R.framework/Versions/3.2/Resources/library/xps/libs/xps.so, 6): Library not loaded: /usr/local/root/lib/root/libGui.so
  Referenced from: /Library/Frameworks/R.framework/Versions/3.2/Resources/library/xps/libs/xps.so
  Reason: image not found
Erreur : le chargement du package ou de l'espace de noms a échoué pour ‘xps’

Sorry but i dont understand why it was so easy to rma normalize affymetrix gene chip array from .cel files (with or without custom cdf) with the affy package in R 2.15 and why it is not possible anymore ? Is there anybody with the same matter ?

thanks again for your answers.

Please see this post of James on why 'affy' cannot handle the new arrays, and you will have to use 'oligo' or 'xps'.

C: oligo package requires the annotation package pd.ht.mg.430.pm - where is it?

You will also find a link in that post that shows you how to analyze new arrays using a custom CDF.

Below some code to get you started normalizing (RMA) your arrays in 'oligo', provided you also have the appropriate probe design (PD) package installed. Also read the vignette!

setwd("/path/to/my/files")
library(oligo)
celFiles <- list.celfiles(full.names = TRUE)
affyExpressionFS <- read.celfiles(celFiles)

ppData <- rma(affyExpressionFS)

write.exprs(ppData, file="myFile.txt", sep="\t")

Ok Thank you very much, i will try your script and take the time to install xps and read the vignette.