[BioC] ComBat

Rama Akondy rama.akondy1 at gmail.com
Tue Jun 10 20:17:56 CEST 2014


Thank you so much for the prompt response. The second row looks skewed and
bimodal (plots attached), would you agree? I tried the non-parametric method
yesterday but basically, the job never finished - I guess that's a gene
pattern issue.


Many thanks again



From: Johnson, William Evan [mailto:wej at bu.edu] 
Sent: Monday, June 09, 2014 1:33 PM
To: Rama Akondy
Cc: bioconductor at r-project.org
Subject: Re: ComBat




Feel free to send me your plots. If your distribution of the means (first
row of plots) are approximately symmetric and bell shaped and the second row
is skewed but not in an overly extreme way---and if there is no bimodality
in these plots--then you will likely not see any difference between the
parametric and non-parametric adjustments. 


Hope this helps,






On Jun 9, 2014, at 1:05 PM, Rama Akondy <rama.akondy1 at gmail.com> wrote:

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.





Rama S.Akondy, Ph.D

Emory University


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