HI all,
I'm having some problem with microarray analysis. I am a biologist not very good with R neither with statistics!
I'm using Agilent 4x44 arrays and the Agi4x44Processed package. I have basically to compare WT vs KO data. The microarray was done first with 3 true biological replicates and later with 4 technical replicates with a pool of RNAs. 
My design is the following:
> targets
FileName	Treat	GErep	Subject	Array Repl.
549_1_4.txt        KO     2	genotype     1   KO1
550_1_4.txt        KO     2	genotype     2   KO2
551_1_4.txt        KO     2	genotype     3   KO3
549_1_3.txt        WT     1	genotype     1   WT1
550_1_3.txt        WT     1	genotype     2   WT2
551_1_3.txt        WT     1	genotype     3   WT3
385_1_1.txt        WT     3	genotype     4   WT4
385_1_2.txt        KO     4	genotype     4   KO4
385_1_3.txt        WT     3	genotype     4   WT4
385_1_4.txt        KO     4	genotype     4   KO4
386_1_2.txt        WT     3	genotype     5   WT4
386_1_3.txt        KO     4	genotype     5   KO4
386_1_4.txt        WT     3 	genotype     5   WT4
I performed normalization and filtering with the entire set of arrays, but when I started the statistical analysis using ebayes with limma I realized I could not treat biological (WT1,2,3-KO1,2,3) and technical replicates (WT4-KO4) the same way. 
I tried to use the dupcor function, but it does not work with tech and biol replicates in the same analysis. Is there a way to bypass the problem? 
Thanks for your help, I really cannot find the way out....
Cheers
Paola 





	[[alternative HTML version deleted]]

