[BioC] dynamic mget with affy annotation

Robert Gentleman rgentlem at fhcrc.org
Thu Jun 9 16:09:12 CEST 2005

You were close it seems -
   mget("1001_at", get(paste("hgu95av2", "SYMBOL", sep="")))

you need to "get" the environment - so you have the object, not the name 
of the object (and you need to make sure you use sep="" in your call to 
paste). Of course there are many other ways to do this (do.call is an 
easy one).

Jacob Michaelson wrote:
> Hi all,
> I'm trying to set up some code that will automatically check the  
> "annotation" component of an exprSet and then properly choose the  
> symbol in an mget statement which will then properly label a heatmap  
> (gene symbols instead of probe ids).  Here's what I've got:
> R>library(annotation(exprset), character.only=T) ##load the proper  
> annotation library
> This is what I want to accomplish (this is how it works without the  
> "dynamic" mget call):
> R>heatmap(exprs(exprset[as.numeric(rownames(topTable 
> (fit2,coef=2,n=50)))]), labRow=mget((topTable(fit2,coef=1,n=50))$ID,  
> env = hgu95av2SYMBOL), col = cm.colors(256))
> I've tried things like "paste" and "cat" to concatenate "<annotation  
> name>" and "SYMBOL" for the env = argument of mget, but nothing seems  
> to achieve the same affect as typing it in.  I've tried everything I  
> can think of, like sticking as.name, as. environment (it complains if  
> it's not an environment) out front.  I know these are just shots in  the 
> dark, but I'm not sure what else to try.
> Any experienced R users have any ideas?
> Thanks in advance,
> Jake
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