[BioC] pm values
Stephen Henderson
s.henderson at ucl.ac.uk
Wed Apr 16 15:05:15 MEST 2003
Hi
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"
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.
--
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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
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