[BioC] boxplot of MM data and normalization

[Shi, Tao]

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.

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

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
>