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

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 > > > >