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Laurent Gautier
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Last seen 10.2 years ago
CCed to bioconductor....
On Wed, Jun 12, 2002 at 04:30:07PM +0200, Jesper Ryge wrote:
> Hi Laurent
>
> I'm using the affy package for R in which it seems you have played a
> role. I'm greatfull that you have developed this tool, but I do
have
> one question I hope you can clarify. When extracting information
from a
> "probe.level.object" there is the variables: id , numbers and names.
Is
Do you mean objects of class "Plob" ?
(if yes, what is 'id' ? if no, which class do you refer to ?)
> it correct that probes with "id==1" has gene name==names[1] - in R
> terms? So that if I for one cell file have called my
>
> > probe.level.object -> data
>
> I will extract probes of PM of id ==1 by:
>
> > PM<-data$pm[id==1]
>
> the order of which will be given by
>
> > numbers[data$id==1]
>
> and all of which correspond to gene
>
> > data$names[1]
>
> Is this correct? It's just to make sure that I do not assign the
wrong
> gene names to the probes...
>
..can't say, the 'id' is mysterious to me...
class?Plob says:
`name': Object of class "character" containing the probe set
identification name (e.g. gene name) of each probe. The
`i'-th entry is the name for the `i'-th row of the matrices
in slots `pm' and `mm'.
`numbers': Object of class "numeric" containing the probe number
of each probe. The `i'-th entry is the number for the `i'-th
row of the matrices in slots `pm' and `mm'.
You may also want to have a look at the function get.PPSet
(try help(get.PPSet)) to do what I suspect you want to do..
Hopin' it helps,
Laurent
> Jesper
>
--
--------------------------------------------------------------
Laurent Gautier CBS, Building 208, DTU
PhD. Student DK-2800 Lyngby,Denmark
tel: +45 45 25 24 85 http://www.cbs.dtu.dk/laurent
