[BioC] Combining two datasets - help to use GeneMeta.

[Sean Davis]

Sharon wrote:
> Hi,
> 
> I am trying to combine two Affy datasets (on rae230a chips), where
> experiments done one year apart. In the first dataset, we have 2
> strains with each strain treated and untreated.  But for the second
> dataset, we have just 2 strains untreated.
> 
> Because of unequal levels in the 2 datasets, I am not able to use
> 'getdF'  in GeneMeta as it is.  Any suggestions for using 'getdF' for
> this situation?  or any alternate way of combining these 2 datasets?

Are these datasets really that much different that you can't just 
combine them?  They may be, but have you looked at affyPLM results, 
density plots, etc., just to be sure?  If they aren't that much 
different, perhaps you can just normalize them together and move on? 
Just asking....

Sean