Question: Removing batch effect from GEO database
gravatar for eric.palanques
8 months ago by
eric.palanques10 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 • 309 views
ADD COMMENTlink modified 8 months ago by Kevin Blighe63k • written 8 months ago by eric.palanques10
gravatar for Kevin Blighe
8 months ago by
Kevin Blighe63k
Kevin Blighe63k 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 8 months ago by Kevin Blighe63k

Thank you very much, that seems to work

ADD REPLYlink written 7 months ago by eric.palanques10
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