[BioC] median of the NUSE value

[kfbargad at ehu.es]

Dear Ben and list,

I have just rerun my code and now it works fine. Sorry for bothering, 
there was probably some typo.

Regards,

David

> 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
> 
>