Hii,

I have 3 batches of samples that belong to 3 conditions/treatments i.e.. batch1(control), batch2(disease stage1), batch3(disease stage2) which belong to the same microarray platform and same tissue.

1) Is there a way to find batch effect for this case ?

2) If so, how can i perform batch adjustment in this case ?

3) Which method should i use to retain biological variation among the batches ?

Please help me out...