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

Hi,

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
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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.

Kevin

ADD COMMENTlink written 6 days ago by Kevin Blighe52k
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