[BioC] pm values
Laurent Gautier
laurent at cbs.dtu.dk
Tue Apr 15 02:29:38 MEST 2003
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
More information about the Bioconductor
mailing list