Hi,

I was thinking about comparing my data set to other publicly available datasets, but they are not on the same platform (mine is Affymetrix Mouse Gene ST 2.0, the other ones are Affymetrix Mouse Gene ST 1.0 or Affymetrix Mouse Genome 430 2.0 Array. 

I would be comparing samples from my arrays to those on other platforms (the groups arent balanced between platforms)

Did some literature search and found some contrasting info about weather or not this is recomended, but I see there are some Bioconductor packages available for this. 

Any recomendations about what to use for this type of analysis (if it is even ok to do this)?