Hi, I don't much experience analyzing microarray data and this is a request
for some information regarding ComBat that I used inGenePattern, basically
to see if I have gone about it correctly.

 

In the new documentation (which is very helpful) : there is a sentence that
describes whether to use the parametric or non-parametric method  "In the
plots, if the black (kernal density estimate of batch effects) and red
(parametric estimate of batch effects) lines do not overlap, then the
non-parametric method should be used."

 

I see 4 plots in my Combat output (using the default parametric method) ,
two of them seem density plots and two Q-Q plots. The lines over in one
density plot and not in the other. Please let me know how to interpret this.

 

Thanks

Rama

 

Rama S.Akondy, Ph.D

Emory University

 

 


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