Dear Sam,

 I am not sure whether this would be a good idea and how it may effect the
statistics but
could you the treat the 6,000 extra probes as missing values and combine the
data to analyse it.
SAM does missing value estimation using kNN.


Regards,
Kishor


On Dec 27, 2007 12:06 AM, Sam Volchenboum <volcs0@gmail.com> wrote:

> I have two sets of data - one done on Affymetrix U133 and another on U133
> Plus 2.0. The data sets are small - 3 control, 3 vector only and 3 vector
> +
> construct for each (so, nine samples total).
>
> Am I better off normalizing and analyzing differential expression within
> each chip separately or is there some way to combine the data? I know I
> can't do this simply because of the 6,000 extra probes on the Plus array,
> but I wanted to see if anyone else had tackled a similar problem.
>
> Thanks.
>
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