Hi, This is my first time working with AffyMatrix .CEL files. I was hoping to extract the probeset gene expression data for the E-MTAB-990 dataset which uses a custom Affymetrix A-AFFY-101. My Code follows the standard pipeline of downloading all files from ArrayExpress and then running gcrma. The problem stems from the error which says "Error in get(probepackagename) : object 'adxcrcg2a520319probe' not found." I have tried looking at makeProbePackage however I'm not sure how to create the "probe_tab" file for A-AFFY-101. The CDF environment is created fine however the last line calling grcma line throws the error.

if (!require("BiocManager", quietly = TRUE))
  install.packages("BiocManager")

BiocManager::install("makecdfenv")
BiocManager::install("affy")
BiocManager::install("ArrayExpress")
BiocManager::install("limma")
BiocManager::install("AnnotationDbi")
BiocManager::install("gcrma")

library("ArrayExpress")
library("makecdfenv")
library("affy")
library("AnnotationDbi")
library("limma")
library("gcrma")

setwd('FOLDER_WITH_CDF_FILE')

make.cdf.package("ADXCRCG2a520319.cdf", "adxcrcg2a520319", species = "Homo sapiens", compress = TRUE)
install.packages("adxcrcg2a520319/", repos = NULL, type = "source")
library("adxcrcg2a520319")

mexp1422 = getAE("E-MTAB-990", type = "full")
rawset <- ReadAffy(cdfname="adxcrcg2a520319")

eset <- gcrma(rawset,type="affinities",fast=FALSE,affinity.source="reference",normalize=TRUE)

To use gcrma you need to have the probe sequences for that array. It doesn't appear that ArrayExpress has the probe sequences, and I don't see any at GEO either. You could try contacting somebody at the Almac Group to see if they have the probe sequences, but otherwise it seems you are out of luck.

That said, gcrma is meant to do a better job of background correcting to remove some bias. However, if you are planning to simply compare the same gene in different conditions, the inherent bias is orthogonal to the comparison (e.g., if a probeset has high GC content, that is true for all of the groups you are comparing), so you don't gain much by controlling for it. In other words, in all my years of analyzing Affy data, I used gcrma only sparingly, and in your case just using rma instead is perfectly fine.