[BioC] Re: order in affy for R

[Laurent Gautier]

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
> 

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