Hi !

I have Gene expression data 76 samples from one chip that is U133a2 and 2 samples from another chip HuGene-2-0.1v2 .

With U133a2 i have 76 cancer samples because i was not getting control so i used control from HuGene-2-0.1v2 .

After normalising seperately  both data from RMA affy package. i manually calculated foldchange by taking average of all 76 samples and 2 control.

Now i want to run one-way unpaired annova and pvalue for this samples .

How can i this.

Thanks!

The short answer is that you can't. Well, you could, but the comparisons are confounded by batch as well as by array. In other words there is no way to say if any differences you might see are due to actual biological differences or simply technical differences between the arrays you are comparing (which are quite different, btw), or differences between the reagents or laboratories, etc.

The technical differences are almost surely much larger than any biological differences for the vast majority of the probesets you want to compare, so you will likely get thousands of differentially expressed probesets, most of which wouldn't be if you were doing something more reasonable.