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Mirza, Nasir
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40
@mirza-nasir-5672
Last seen 10.5 years ago
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
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