[BioC] Limma. How can I deal with two sets with different printing.

[M PEREZ]

Hi list,

 

I have five replicates comparing wt vs. mut. 

 

But 3 slides came from one printing and the other two came from other different printing (both from the same company and the most of the genes are the same in both sets). I am not sure how can I deal with them using Limma.

 

I assume that it is not possible to perform a global print-tip loess normalization, so, Could be it possible to normalize the two set independently and after that joint both datasets in just one, and then apply Linfit and ebayes? . I appreciate any suggestion

 

Thank you.

Manuel

 
 

		
---------------------------------


	[[alternative HTML version deleted]]