Hi, 

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!

Best, 

Nina

The QC functions that are missing are mainly those that pertain to things like 5' vs 3' bias, which made sense in the context of a 3' biased array, but no longer really make sense in the context of a random primer based array. In addition, there aren't any MM probes on these arrays (they were even going away from the MM probes in the 3' biased era), so it's difficult to generate a meaningful background binding plot.

In my experience, a density plot of the raw data, an NUSE plot, and a PCA plot will tell you pretty much everything you need to know about the quality or usefulness of your data.