[BioC] pm values

Stephen Henderson s.henderson at ucl.ac.uk
Wed Apr 16 15:05:15 MEST 2003

 Thanks for your help. Unfortunately this is not doing as I expected. Ia m
on Windows,  affy version 1.1.1 and 
> R.version.string
[1] "R version 1.6.1, 2002-11-01"


> bigbatch2
AffyBatch object
size of arrays=712x712 features (209917 kb)
cdf=HG-U133A (22283 affyids)
number of samples=53
number of genes=22283

[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
ProbeSet object:
  pm= 11 probes

ProbeSet object:
  pm= 11 probes

... etc

Where are the expected probe values? Do I need to change to the devel.

-----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
> etc. What do I need to be doing?
> Thanks
> 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.

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

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,

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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