Hi!

I am analysing CEL files from an Affimetrix HTA 2.0 array. The package affy works with older arrays, but for this model I had to use oligo package; which, instead of creating an AffyBatch object when reading the files, it creates an HTAFeatureSet. This object is not compatible with arrayQualityMetrics.

Is it any way of using this function with this type of objects? Or is it any similar package which suits HTAFeatureSet objects?

Thanks!

There isn't a package like arrayQualityMetrics that is intended for these arrays, although I assume you could recapitulate some of the things that arrayQualityMetrics does. There is a vignette about advanced things you can do that might be helpful. There is also an entire section in the oligo vignette devoted to quality control that you might read.