[BioC] selecting probe set from expression matrix

[Rhonda DeCook]

srini,

It seems like there's a lot of ways to pull-out information for a specific gene 
depending on the type of object you're working with.  The vignettes should help 
you here.  Once you're working with a matrix like 'ex.data', a not so elegant 
way is by getting the probeset names with... 
> dimnames(ex.data)[[1]]

Then you can pull out the rows(genes) you want from the expression set using a 
boolean vector:
> ex.data[as.logical(dimnames(ex.data)[[1]]=="267644_s_at"),]

This should give you the expression measure for each chip at the given gene as 
a numeric vector.

_____________

To find out the type of an object called 'ex.data', type...
> mode(ex.data)
You can also ask if it is something, like...
> is.matrix(ex.data)

Rhonda





> dear list,
> 
> I generated expressions for a study in the following
> way.
> 
> rm.data <- justRMA()
> ex.data <- exprs(rm.data)
> 
> Now I want to select 217523_at, 212063_at,
> 212014_x_at. 
> 
> How can I select these probesets. 
> 
> > dim(data)
> [1] 22283   158
> 
> 
> 2 question: how do I know data is which type of
> object. 
> 
> thank you
> srini
> 
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