[BioC] pm values

[Laurent Gautier]

On Mon, Apr 14, 2003 at 03:18:58PM +0100, Stephen Henderson wrote:
> Sorry I have been looking through the vignette on Affy but am still a bit
> confused hot to extract the probe level data I need. 
> 
> I have an AffyBatch object with ca 43 (U133A) samples. Ihave 5 genes of
> interest that I wish to examine the probes. 
> 
> >Bigbatch
> 
> > genes
> [1] "blahbla_s_at" "blahbla_s_at" "blahbla_s_at" "blahbla_s_at" 
> [5] "blahbla_s_at"
> 
> I then try 
> >place<- pmindex(bigbatch, genes)
> 
> or even 
> >place<- pmindex(bigbatch, genes, xy=TRUE)
> 
> This gives me a list of 5 sets of vectors, or 5 sets of coordinates.
> 
> Now when I try 
> 
> >pm(bigbatch)[place[[1]]]
> or all sorts of variants e.g.
> 
> pm(bigbatch)[,place[[1]]]
> 
> I don't get the probes I am looking for at all "blahbla_s_at1 "blahbla_s_at2
> etc. What do I need to be doing?
> 
> Thanks
> Stephen
> 
>  

Stephen,

I'll assume that you are interested in the probe intensities
(rather than say the probe locations on the chip). 

The class ProbeSet is your friend.
Try:

ppsets <- probeset(bigbatch, genes)
par(mfrow=c(3,3)); par(ask=TRUE)
barplot(ppsets[[1]])


Note: the argument 'xy=TRUE' in pmindex is deprecated. It's use
is discouraged, and it should disappear sometimes.
Note (bis): Few things were improved for the ProbeSet since the 
last release. The devel version of the pack could well be worth
a look.


Hopin' it helps,




L. 
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Laurent Gautier			CBS, Building 208, DTU
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