Hi all, I'm trying to create an AffyBatch object from ArrayExpress experiment, so I'm following the instructions in vignette of ArrayExpress, but the output of ArrayExpress() function on an Affymetrix experiment (E-MEXP-1422, this accession is give the instruction) is always of type ExpressionFeatureSet. So my question is: the ArrayExpress() function use the oligo package to download and handling the experiment in ArrayExpress repository?

Thank you very much for your help

ArrayExpress by default will use the oligo package to read in Affymetrix celfiles, because the oligo package can handle all Affymetrix arrays, whereas the affy package cannot. Do you have a particular use case that requires the affy package? If so, you can use getAE to get the raw data, and then process as you like.