Question: Is Batch correction required for the same micro array platform?
0
gravatar for au.rinki.bio
11 weeks ago by
au.rinki.bio10
University of Allahabad, India
au.rinki.bio10 wrote:

Hii I am handling microarray data and I have two datasets with the same platform (GPL750) one of which contains tumor samples and another one has normal samples. I want to merge these two datasets for differential expression analysis. Is it required batch correction?

microarray meta analysis • 122 views
ADD COMMENTlink written 11 weeks ago by au.rinki.bio10
2

Before to think about batch correction I suggest considering this: Do you have replicates? How dispersed they are? what are the causes of the batch effect? Do I have the batch effect?. If you don't have replicates, Is it possible to have the batch effect without replicates?

ADD REPLYlink written 11 weeks ago by Buffo1.7k
1
gravatar for Benn
11 weeks ago by
Benn7.9k
Netherlands
Benn7.9k wrote:

If the data is from two different experiments, you should correct for batch effect indeed. It sounds however, that you have an impossible design: tumors in one batch and normal in the other batch. It is not possible to correct for batch in this case, since there is no overlap between the batches. You need tumors and/or normals in both batches.

ADD COMMENTlink modified 11 weeks ago • written 11 weeks ago by Benn7.9k

sorry for the very basic question can I consider normal and case sample from different dataset? is it valid for differential expression analysis?

ADD REPLYlink written 11 weeks ago by au.rinki.bio10
1

No that would not be wise and sound, since you can't distinguish between real effect (between normal and tumor) and between batch effect.

ADD REPLYlink written 11 weeks ago by Benn7.9k

In this case how to remove batch effect?

ADD REPLYlink written 11 weeks ago by au.rinki.bio10
1

Sorry, not possible.

ADD REPLYlink written 11 weeks ago by Benn7.9k
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