Question: Removing batch effect from GEO database
gravatar for eric.palanques
6 days ago by
eric.palanques0 wrote:


I have downloaded several GSE from GEO database, all from Homo sapiens and from the same platform and tissue. I have merged all the datasets and performed RMA normalization on the merged set. However, I can still see a lot of unexpected variation between them. I suppose it is due to batch effect. How could I remove it?

Thanks in advance,

batch effect geo • 49 views
ADD COMMENTlink modified 6 days ago by Kevin Blighe52k • written 6 days ago by eric.palanques0
gravatar for Kevin Blighe
6 days ago by
Kevin Blighe52k
Kevin Blighe52k wrote:

If you believe there are 'extraneous' effects / unwanted sources of variation in the dataset that could bias your results, then you could perform Surrogate Variable Analysis, which will essentially identify a set of variabes that 'capture' this unwanted variation. The idea, then, is to include these variables in your design forumla for the purpose of controlling for these.


ADD COMMENTlink written 6 days ago by Kevin Blighe52k
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