[BioC] as.numeric and NA

[Kasper Daniel Hansen]

What Wolfgang is implying is that it is a rather strange thing you want 
to do. Your command was
  as.numeric(sampleNames(data.raw))
with data.raw an AffyBatch object. Now, 
  sampleNames(data.raw)
will return you a vector of sampleNames, which is a character vector 
with names associated with each sample. I believe the default is to put 
the filenames there. So the command
  sampleNames(data.raw)
should return a vector of filesnames. It is not at all clear how these 
filenames should be converted to numbers. Compare
  > as.numeric(c("1","2","3"))
  [1] 1 2 3
  > as.numeric(c("a","b","c")) 
  [1] NA NA NA
  Warning message:
  NAs introduced by coercion


Kasper


On Mon, May 30, 2005 at 01:47:49PM +0200, Mohammad Esad-Djou wrote:
> Thank you for your answer.  
> 
> > have you tried
> > 
> > 	exprs(data.raw) or
> > 	intensity(data.raw)
> > 
> Yes, I already tried exprs(data.raw).  
> Unfortunately does not help me. I simplified my question, so that it can be answered concretely.
> I will read again R manual. 
> 
> best Regards,
> Mohammad
> 
> 
> 
> Wolfgang Huber <huber at ebi.ac.uk> schrieb am 30.05.05 13:18:38:
> > 
> > Mohammad,
> > 
> > Also, please consider that the software is written by and the mailing 
> > list discussions are provided by volunteers. So before posting such a 
> > question, please consider reading the vignette of the affy package 
> > first, and perhaps a manual of the R language.
> > 
> > Best wishes
> >   Wolfgang
> > 
> > Mohammad Esad-Djou wrote:
> > > Hello, 
> > > 
> > > I would like to use for 42 experiments "as.numeric" (objects of type '"numeric"')
> > > I wrote in such a way:
> > > 
> > > 
> > >>library(affy)
> > >>data.raw <- ReadAffy(filenames= "./R/ME_cel/Expt1_R1.CEL",
> > > 
> > > ...    "./R/ME_cel/Expt14_R3.CEL")
> > > 
> > > 
> > >>as.numeric(sampleNames(data.raw))
> > > 
> > >  [1] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> > > [26] NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA NA
> > > Warning message:
> > > NAs introduced by coercion
> > > 
> > > 
> > > How can I find correctly numeric values of data.raw?
> > > 
> > > Thanks,
> > > Mohammad Esad-Djou
> > > 
> > >
> > 
> > 
> > Best regards
> >    Wolfgang
> > 
> > -------------------------------------
> > Wolfgang Huber
> > European Bioinformatics Institute
> > European Molecular Biology Laboratory
> > Cambridge CB10 1SD
> > England
> > Phone: +44 1223 494642
> > Fax:   +44 1223 494486
> > Http:  www.ebi.ac.uk/huber
> > -------------------------------------
> 
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-- 
Kasper Daniel Hansen, Research Assistant
Department of Biostatistics, University of Copenhagen