Does anyone have any idea how to map the probesets between Affymetrix U133plus2 and Human Exon ST 1.0 microarray? Is there any useful bioconductor package or bioinformatics program?
The easiest method is to find the intersect of identical probe sequences, note they do not always map 1 to 1.
Have you checked NetAffx (database by Affymetrix) generally they have such information (which can be downloaded)?
you can also check biomart id converter
http://central.biomart.org/converter/#!/ID_converter/gene_ensembl_config_2
There is no 1-1 mapping, as 133p2 has mainly 3' and Exon has probes all across transcripts and not only.
To compare those two types of microarrays summarize them into the same level (eg Ensembl gene) using Brainarray
CDFs (http://brainarray.mbni.med.umich.edu/Brainarray/Database/CustomCDF/CDF_download.asp) and fish out
those that have expression values on both (and use a bathch correction like pamr.batchadjust() in R)
To visually see where the probes on both chips are targeting, you can use Annmap browser:
http://annmap.picr.man.ac.uk/
switching between array type for your favourite genes. Have fun ! :)
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