[BioC] boxplot of MM data and normalization

[James W. MacDonald]

Shi, Tao wrote:
> Hi list,
> 
> My first question is a follow-up of an old post (
> https://stat.ethz.ch/pipermail/bioconductor/2003-October/002660.html
> ).  I don't think boxplot(myDat, with="MM") works.  Please see below.
> I'm using R 2.3.0,  WinXP, affy 1.10.0.

You are correct; with = "MM" doesn't work because R is case sensitive, 
and the correct argument is "mm".

> 
> My second question is: do differenet normalization options in
> 'expresso' do anything to the MM probes?

Well, a quick look at ?normalize.loess gives this:

Details:

      The type arguement should be one of
      '"separate","pmonly","mmonly","together"' which indicates whether
      to normalize only one probe type (PM,MM) or both together or
      separately.

Looking at the help pages for the other methods may be just as helpful ;-P

Best,

Jim


> 
> thanks,
> 
> ...Tao
> 
> 
> 
>> data(affybatch.example) par(mfrow=c(1,2)) 
>> boxplot(affybatch.example, with="PM") boxplot(affybatch.example,
>> with="MM")
>> 
>> boxplot(affybatch.example, with="PM")$stat
> 
> [,1]      [,2]      [,3] [1,]  6.175924  5.672425  5.942515 [2,]
> 6.794416  6.375039  6.574404 [3,]  7.179909  6.870365  6.954196 [4,]
> 8.321921  7.927185  8.053383 [5,] 14.176664 13.515946 14.188434
> 
>> boxplot(affybatch.example, with="MM")$stat
> 
> [,1]      [,2]      [,3] [1,]  6.175924  5.672425  5.942515 [2,]
> 6.794416  6.375039  6.574404 [3,]  7.179909  6.870365  6.954196 [4,]
> 8.321921  7.927185  8.053383 [5,] 14.176664 13.515946 14.188434
> 
>> 
>> boxplot(data.frame(log2(pm(affybatch.example))))$stat
> 
> [,1]     [,2]     [,3] [1,] 6.175924 5.700440 5.942515 [2,] 6.768184
> 6.345183 6.549205 [3,] 7.108524 6.791814 6.882643 [4,] 8.012624
> 7.660353 7.749199 [5,] 9.878051 9.612868 9.541097
> 
>> boxplot(data.frame(log2(mm(affybatch.example))))$stat
> 
> [,1]      [,2]      [,3] [1,]  6.205549  5.672425  5.995485 [2,]
> 6.820179  6.397461  6.589464 [3,]  7.285402  6.965784  7.056908 [4,]
> 8.657851  8.224002  8.359309 [5,] 11.398904 10.959278 10.990104
> 
> 
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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623


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