[BioC] dynamic mget with affy annotation

Jacob Michaelson jjmichael at comcast.net
Thu Jun 9 15:53:40 CEST 2005

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):

(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,


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