[BioC] Replace method, AffyBatch, pm or mm

[Rafael A. Irizarry]

the error here is the use of ",psn". it seems like you made a mistake
when typing "exp.norm,psn". did you mean "exp.norm.psn"?

functions think psn is an argument. pm has
a ... in the args so it passes it as part of ... and ignores.  but pm<-
doesnt have a ... so you get an error.

as far as i know all the multigets where removed some time ago. what
version are you using? if you find a multiget in >=1.5 please let me know.


On Tue, 19 Oct 2004, Robert Gentleman wrote:

> On Tue, Oct 19, 2004 at 10:08:06AM +0200, Laurent Buffat wrote:
> > Hi everyone,
> > 
> > In an affybatch, I can extract from an affybatch “exp.norm” and a given
> > probesetname, psm, the pm value for a list of condition :
> > 
> > > pm(exp.norm,psn)[,1:3]    
> > 
> >                     1          2          3
> > 
> > 1007_s_at1  501.35097 430.517639 495.100973
> > 
> > 1007_s_at2  120.76764 131.600973 142.100973
> > 
> > 1007_s_at3  293.51764 290.017639 268.350973
> > 
> > 1007_s_at4  517.43431 568.184306 635.184306
> > 
> > …. Etc…
> > 
> >  
> > 
> > Now, I would like to replace these values by an over one like for example :
> > 
> >  > pm(exp.norm,psn)[,1:3] <- pm(exp.norm,psn)[,1:3] + 1000
> > 
> > or
> > 
> > *       pm(ex.norm,psn)[,1:3] <- NA
> > 
> > But, I have these error :
> > 
> > > pm(exp.norm,psn)[,1:3] <- pm(exp.norm,psn)[,1:3]
> > 
> > Error in "pm<-"(`*tmp*`, psn, value = pm(exp.norm, psn)[, 1:3]) :
> > 
> >         unused argument(s) ( ...)
> > 
> > In addition: Warning messages:
> > 
> > 1: 'multiget' is deprecated.
> > 
> 
>   so, for the multiget part, that is something the author/maintainer
>   should have already dealt with. The R function multiget is
>   deprecated (and in fact in R 2.0.0 it no longer exists, so this code
>   will not work there). Nothing bad happens in the present case, it
>   works as it did before, it is just a warning for the software
>   developer to please change their code (they usually get about 1 year
>   to do so).
> 
> > Use 'mget' instead.
> > 
> > See help("Deprecated") and help("base-deprecated").
> > 
> > 2: 'multiget' is deprecated.
> > 
> > Use 'mget' instead.
> > 
> > See help("Deprecated") and help("base-deprecated").
> > 
> >  
> > 
> > Thanks for your help.
> > 
> >  
> > 
> > Laurent Buffat
> > 
> >  
> > 
> >  
> > 
> >  
> > 
> >  
> > 
> >  
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> >  
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> >  
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> >  
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> >  
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> > 
> > 	[[alternative HTML version deleted]]
> > 
> > _______________________________________________
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> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> 
> -- 
> +---------------------------------------------------------------------------+
> | Robert Gentleman                 phone : (617) 632-5250                   |
> | Associate Professor              fax:   (617)  632-2444                   |
> | Department of Biostatistics      office: M1B20                            |
> | Harvard School of Public Health  email: rgentlem at jimmy.harvard.edu        |
> +---------------------------------------------------------------------------+
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