I wanna analyze dataset produce by Rosetta/Merck Human RSTA Custom Affymetrix 2.0 microarray, which annotationData package should I use?
We only supply annotation packages for the commercially available Affy arrays. Do you have access to the transcript annotation CSV file?
I am not sure if this is useful, but since I am using array express, there is an array_design file, A-GEOD-15048.adf.txt. Can I use this for annotation?
Yes. You could either parse out the probeset and RefSeq IDs and use the AnnotationForge package to make an annotation package that you could install. Alternatively, if the data are actually on ArrayExpress or GEO, you could use the ArrayExpress or GEOquery packages to download, in which case you end up with an ExpressionSet with the annotation data in the fData slot. If you use things like limma for downstream analysis, you will automatically get whatever is in the fData slot in your output.
So you could hypothetically get the annotation 'for free', but do note that what you get in the adf file (and also what you get from GEO) is usually way more than you really want, so it's helpful to cut down to just the columns that interest you.