Problem with Combat batch adjustment
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vinnu260 ▴ 10
@vinnu260-11958
Last seen 4.6 years ago

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...

combat sva • 518 views
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You cannot use COMBAT when your data is 100% confounded like that.

I have the same problem, because everything was done in the same lab and same platform and same people for me we are just assuming batch effect does not exist. This is bad experimental design.

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Thanks
 

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