[BioC] median of the NUSE value

[Ben Bolstad]

Below is my results using affyPLM 1.9.5.  No particular problem here
with that version. What was your fitPLM call?







> Pset <- fitPLM(Dilution)
Background correcting PM
Normalizing PM
Fitting models
> NUSE(Pset,main="NUSE values",col=rainbow(4))
>  NUSE(Pset,type="stats")
              20A        20B        10A        10B
median 0.99929158 0.99939860 1.00213287 0.99927522
IQR    0.02592881 0.02963567 0.02816327 0.02591606
>  NUSE(Pset,type="stats")
              20A        20B        10A        10B
median 0.99929158 0.99939860 1.00213287 0.99927522
IQR    0.02592881 0.02963567 0.02816327 0.02591606

On Thu, 2006-06-15 at 13:11 +0200, kfbargad at ehu.es wrote:
> Dear list,
> 
> I am using affyPLM for my QC, and am trying to obtain the median of 
> the NUSE values for my chips.
> 
> if I type 
> >NUSE(Pset, main = "NUSE values") 
> I get the NUSE boxplot
> 
> but if I type
> > NUSE(Pset, type = "stats")
> Error in match.arg(type) : 'arg' should be one of plot, values
> or
> > NUSE(Pset, type = "values")
> Error in x at weights[which, ] : incorrect number of dimensions
> In addition: Warning messages:
> 1: longer object length
>         is not a multiple of shorter object length in: model == (PM ~ -
> 1 + probes + samples) 
> 2: longer object length
>         is not a multiple of shorter object length in: model == (PM ~ -
> 1 + samples + probes) 
> 3: the condition has length > 1 and only the first element will be 
> used in: if ((model == (PM ~ -1 + probes + samples)) | (model == (PM ~
> 
> my sessionInfo()
> Version 2.3.0 (2006-04-24) 
> i386-pc-mingw32 
> 
> attached base packages:
> [1] "stats"     "graphics"  "grDevices" "utils"     "datasets"  "tools"
>      "methods"   "base"     
> 
> other attached packages:
> hgu133plus2cdf        affyPLM          gcrma    matchprobes       
> affydata           affy         affyio        Biobase 
>       "1.12.0"        "1.8.0"
> 
> 
> Any suggestions??
> 
> Also, is it possible to colour the boxes of the boxplot? I have so far 
> been using 
> boxplot() for Pset with the argument "col", but it does not work for 
> NUSE()
> 
> 
> Thanks in advance,
> 
> David
> 
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-- 
Ben Bolstad <bmb at bmbolstad.com>
http://bmbolstad.com