[BioC] ComBat: Comparison of data

[W. Evan Johnson]

Interesting question! Yes I should still have the code. For reference, do you want the code so you can recreate the results of my paper, or so that you can make these plots for your data? If the former, I'll have to post my normalized data and the code. If the latter I can just email you the code. 



On Oct 29, 2012, at 10:40 AM, Peter Kupfer wrote:

> Thanks Evan!
> So I did the right comparison methods in the past. 
> Further question: Is there any possibility to get the code which you used to plot the shrinkage plots as showed in your paper?
> Thanks and all the best
> Peter
> 
> 
> 
> 
> Am 29.10.2012 um 15:39 schrieb "W. Evan Johnson" <wej at bu.edu>:
> 
>> Peter, 
>> 
>> Use hierarchical clustering for before and after to see if the samples cluster by batch. Also many people like to plot the principle components to see if there is separation by batch in some of the components. Finally, if you have only a couple batches, you could try to predict batch based on the data and see if this is different between the corrected and uncorrected data.
>> 
>> Thanks!
>> 
>> Evan
>> 
>> 
>> 
>> On Oct 29, 2012, at 6:35 AM, Peter Kupfer wrote:
>> 
>>> Dear all,
>>> i deal with the tool ComBat and try to remove underlying batch effects. Therefor I used covariates and recommend in the manual. 
>>> After correcting the data and want to have a glue, what the tool did. Therefor i am looking for a method for comparing the corrected and the uncorrected data. 
>>> Is there any method for such comparison which you would suggest? Furthermore I am looking for the R code for the (so called) shrinkage plots. 
>>> Would be amazing if anybody could give me some ideas to compare the outcome of ComBat with my input.
>>> Thanks in advance and all the best from Germany
>>> Peter Kupfer
>>> 
>>> 
>>> 
>>> 
>>> 
>> 
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>