[BioC] Replace method, AffyBatch, pm or mm

[Robert Gentleman]

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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> 	[[alternative HTML version deleted]]
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-- 
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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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