[BioC] Replace method, AffyBatch, pm or mm

[Rafael A. Irizarry]

sorry, i now see what psn is. 

to increase speed, the current implementation only lets you replace all
the pm. that is  feautre that we could add. for now you can do by using 
pm(abatch)[,index] <- value

-r


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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> > 
> > 	[[alternative HTML version deleted]]
> > 
> > _______________________________________________
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> 
> -- 
> +---------------------------------------------------------------------------+
> | 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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