I am trying to analyze data from Affymetrix GeneChip Mouse Gene 2.0 ST Array. I am using "oligo" package to import .CEL files, preprocess and do QC, but I noticed that oligo package has a limitted selection of QC stats compred to simpleAffy and affyQCReport (which I cant use because I cant import this type of array with "affy" package to create affyBatchObject).
I was wondering if there was a reason why some of those functions are not available in oligo (array desing change makes them inappropriate?) or is there a way to do them in another package?
I am quite new to this so I am not even sure what are the "recomended" qc stats and graphs to check array quality? As I see, "oligo" package offers image, hist, boxplot and MAplot functions for visualization and QC and NUSE and RLE plots can also be done - is that enough to check for quality?
A lot of questions - ANY input on this will be great!