Hello,

I would like to remove the batch effects from a gene expression data using
Surrogate Variable Analysis (SVA).  When I looked at the SVA (
http://www.bioconductor.org/packages/release/bioc/html/sva.html) and
"bladderbatch", I noticed that for 57 different samples, there are 5
different batches.  May someone let me know how I could define these
batches for my own data?  In fact, my datasets include the normal, disease,
two different tissues, and two different chip arrays?

Thanks,

Jerry

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