[BioC] boxplot of MM data and normalization

[James W. MacDonald]

Sorry; which = "pm", not with.

Jim



Shi, Tao wrote:
> 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
> 
> 
> 
> 
>> _______________________________________________ Bioconductor
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> 
> 
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> 
> 
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> 
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> 
> 
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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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