[BioC] Re: order in affy for R

[Rafael A. Irizarry]

jesper, what version of the package are you using? the latest is 1.0.1

rafael
On Thu, 13 Jun 2002, 
Laurent Gautier wrote:

> 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
> > 
> 
>