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Question: Adjusting microarray data using ComBat and SVA
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gravatar for Mirza, Nasir
5.9 years ago by
Mirza, Nasir40
Mirza, Nasir40 wrote:
Hello My microarrays were processed in batches. I would like to remove batch effect using ComBat. But I also want to adjust for unknown sources of noise using sva. Is there a way of combining these two methods? I could run ComBat first, get the ComBat-adjusted matrix, and run sva on this, but I am concerned if it is bad practice to run a second adjustment on data which has already been adjusted by a different package. Is it possible perhaps to include the surrogate variables from SVA in the model matrix for ComBat? Or is there a better way of combining the methods? Please note that I would prefer to use ComBat to remove batches, rather than use batch as an adjustment variable in sva, as ComBat does a better job of removing batch effect from my data. Thank you! Nasir [[alternative HTML version deleted]]
sva
ADD COMMENTlink modified 2.6 years ago by cathytian20110 • written 5.9 years ago by Mirza, Nasir40
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gravatar for cathytian2011
2.6 years ago by
cathytian20110 wrote:

Hi,Nasir,

I have the same problem. Do you find a solution to your problem?

Best,

Fuying

ADD COMMENTlink written 2.6 years ago by cathytian20110
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