[BioC] pm values

[Stephen Henderson]

Ah thank you.
 that's what we need!

Cheers
Stephen

-----Original Message-----
From: Laurent Gautier [mailto:laurent at cbs.dtu.dk] 
Sent: Wednesday, April 16, 2003 2:26 PM
To: Stephen Henderson
Cc: 'Laurent Gautier'; bioconductor at stat.math.ethz.ch
Subject: Re: [BioC] pm values

On Wed, Apr 16, 2003 at 02:05:15PM +0100, Stephen Henderson wrote:
> Hi
>  Thanks for your help. Unfortunately this is not doing as I expected. Ia m
> on Windows,  affy version 1.1.1 and 

However, a glance at what is below makes me believe it does what I expect.
In the example, ppsets is a 'list' of elements of class 'ProbeSet'
(class?ProbeSet to know more about it, like where are the probe intensities
(Would something like ppsets[[i]]@pm do what you expect ?)).


> > R.version.string
> [1] "R version 1.6.1, 2002-11-01"
> 
> So
> 
> > bigbatch2
> AffyBatch object
> size of arrays=712x712 features (209917 kb)
> cdf=HG-U133A (22283 affyids)
> number of samples=53
> number of genes=22283
> annotation=hgu133a
> notes=
> 
> > EWS
> [1] "209214_s_at" "210011_s_at" "210012_s_at" "210581_x_at" "211391_s_at"
> [6] "211603_s_at" "211825_s_at"
> 
> > ppsets<-probeset(bigbatch2, EWS)
> 
> > ppsets
> $"209214_s_at"
> ProbeSet object:
>   id=209214_s_at
>   pm= 11 probes
> 
> $"210011_s_at"
> ProbeSet object:
>   id=210011_s_at
>   pm= 11 probes
> 
> ... etc
> 
> Where are the expected probe values? Do I need to change to the devel.
> version?
> 
> -----Original Message-----
> From: Laurent Gautier [mailto:laurent at cbs.dtu.dk] 
> Sent: Tuesday, April 15, 2003 12:30 AM
> To: Stephen Henderson
> Cc: bioconductor at stat.math.ethz.ch
> Subject: Re: [BioC] pm values
> 
> 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. 
> -- 
> --------------------------------------------------------------
> currently at the National Yang-Ming University in Taipei, Taiwan
> --------------------------------------------------------------
> Laurent Gautier			CBS, Building 208, DTU
> PhD. Student			DK-2800 Lyngby,Denmark	
> tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent
> 
> 
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-- 
--------------------------------------------------------------
currently at the National Yang-Ming University in Taipei, Taiwan
--------------------------------------------------------------
Laurent Gautier			CBS, Building 208, DTU
PhD. Student			DK-2800 Lyngby,Denmark	
tel: +45 45 25 24 89		http://www.cbs.dtu.dk/laurent