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@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
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