[BioC] normalize.AffyBatch.quantiles and NA values

[odlc at uchicago.edu]

Ben,

Thank you very much for the answer.

By the way, I got your name wrong in my posting. For 
the record, for those who might read this: the correct
reference for the quantile normalization procedure for
microarrays is:

 Bolstad et al., Bioinformatics, 19(2):185–193, Jan 2003

Sorry for the confusion,

Omar.


---- Original message ----
>Date: Wed, 05 Jul 2006 09:16:08 -0700
>From: Ben Bolstad <bmb at bmbolstad.com>  
>Subject: Re: [BioC] normalize.AffyBatch.quantiles and NA values  
>To: odlc at uchicago.edu
>Cc: bioconductor at stat.math.ethz.ch
>
>Your understanding of what the code is doing is correct. eg
>
>> data(affybatch.example)
>> pm(affybatch.example)[1,]
>20A 20B 10A
>149 118 124
>> pm(affybatch.example)[1,1] <- NA
>> affybatch.example.norm <- normalize(affybatch.example)
>> pm(affybatch.example)[1:3,]
>       20A   20B   10A
>[1,]    NA 118.0 124.0
>[2,] 143.5 124.8 116.5
>[3,] 132.0 111.0 105.0
>> pm(affybatch.example.norm)[1:3,]
>          20A      20B      10A
>[1,]       NA 118.0000 124.0000
>[2,] 127.2667 137.3667 120.1667
>[3,] 115.8333 122.6000 107.3333
>>
>
>
>Note that normalize calls normalize.AffyBatch.quantiles by
default in
>this case. 
>
>Why does it do this? Because the underlying routine which
does the
>normalization normalize.quantiles() does not handle NA
values. In some
>sense this was done by design, the thinking being that if you
start off
>with raw CEL file data there should not be any missing data.
>
>
>Ben
>
>
>On Fri, 2006-06-30 at 09:33 -0500, odlc at uchicago.edu wrote:
>> Hello,
>> 
>> I am trying to understand how normalize.AffyBatch.quantiles
>> works. From what I understand of the code, it seems that
>> rows (corresponding to a probe) which contain even a single
>> NA are dropped; then, the quantile-normalization method 
>> described in Botstein et al. is applied to the remaining rows,
>> and these normalized rows are put back into the original
>> batch. 
>> 
>> In other words, values in a row that contains NA's
>> remain unchanged.
>> 
>> Questions:
>> 
>> - Is this really how it works?
>> 
>> - If yes, is this the intended behavior?
>> 
>> Thank you,
>> 
>> Omar.
>> 
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>-- 
>Ben Bolstad <bmb at bmbolstad.com>
>http://bmbolstad.com
>