Hi Meraj,

One clarification: the Bscore method in cellHTS2 does not automatically divide by the MAD. One must explicitly specify varianceAdjust="byPlate" to enforce this.

Best wishes,
Joseph


On Jun 11, 2012, at 8:37 PM, Joseph Barry wrote:

> Hi Meraj,
> 
> I would recommend that you use the method="median" and varianceAdjust="byPlate" (or alternatively "byExperiment" or "byBatch", depending on the context) options to normalizePlates. This will subtract the median and divide by the median absolute deviation (MAD), which is slightly more robust than the classical zscore, where one subtracts the mean and divides by the standard deviation.
> 
> The Bscore normalization method subtracts the plate median and divides by the plate MAD, but also applies a two-way median polish to correct for row and column effects. Thus it is essentially a zscore with a few more bells and whistles attached, if you will. The references at the bottom of the ?Bscore documentation explain this in more detail and will help you to decide whether or not this is appropriate for your data.
> 
> (cc'd to the bioconductor mailing list for future googlers :) )
> 
> Best wishes,
> Joseph
> 
> On Jun 11, 2012, at 8:11 PM, <maziz@tgen.org> <maziz@tgen.org> wrote:
> 
>> Hi Joseph
>>  
>> I have a question regarding the scores generated by cellhts2.
>> I would really appreciate if you can answer them.
>>  
>> In your paper
>> http://genomebiology.com/content/pdf/gb-2006-7-7-r66.pdf
>> you mention zscore as the basis of your score. Online
>> cellhts2 does not have a zscore normalization mechanism/option.
>>  
>> Question is:
>> 1)     How can I only choose zscore normalization.
>> 2)     And if I choose Bscore normalization. Is the score really standard
>> deviation from the mean/median.
>>  
>> In the R_OUTPUT file I see:
>> NormalizationMethod="Bscore"
>> Score="zscore"
>> (what exactly does this imply)
>>  
>> Thank you for your help
>>  
>> Meraj
> 


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