[BioC] boxplot of MM data and normalization

[Shi, Tao]

Hi Jim,

Thanks for the quick reply!

With the lower case letters, I don't think it's working either.  See below.

Regarding my second question, I would assume 'expresso' uses the default parameters, which should be 'separate' for 'type' in most cases, for the normalization method it specified when no 'normalize.param' are supplied?

best,
...Tao


> data(affybatch.example)
> par(mfrow=c(1,2))
> 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





----- Original Message -
From: James W. MacDonald <jmacdon at med.umich.edu>
To: "Shi, Tao" <shidaxia at yahoo.com>
Cc: bioconductor at stat.math.ethz.ch
Sent: Tuesday, October 3, 2006 12:35:21 PM
Subject: Re: [BioC] boxplot of MM data and normalization

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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