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 ********************************************************************** This email and any files transmitted with it are confidential an... {{dropped}}

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

Hi Thanks for your help. Unfortunately this is not doing as I expected. Ia m on Windows, affy version 1.1.1 and > R.version.string [1] "R version 1.6.1, 2002-11-01" So > bigbatch2 AffyBatch object size of arrays=712x712 features (209917 kb) cdf=HG-U133A (22283 affyids) number of samples=53 number of genes=22283 annotation=hgu133a notes= > EWS [1] "209214_s_at" "210011_s_at" "210012_s_at" "210581_x_at" "211391_s_at" [6] "211603_s_at" "211825_s_at" > ppsets<-probeset(bigbatch2, EWS) > ppsets $"209214_s_at" ProbeSet object: id=209214_s_at pm= 11 probes $"210011_s_at" ProbeSet object: id=210011_s_at pm= 11 probes ... etc Where are the expected probe values? Do I need to change to the devel. version? -----Original Message----- From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] Sent: Tuesday, April 15, 2003 12:30 AM To: Stephen Henderson Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] pm values 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 ********************************************************************** This email and any files transmitted with it are confidential an... {{dropped}}

Ah thank you. that's what we need! Cheers Stephen -----Original Message----- From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] Sent: Wednesday, April 16, 2003 2:26 PM To: Stephen Henderson Cc: 'Laurent Gautier'; bioconductor@stat.math.ethz.ch Subject: Re: [BioC] pm values On Wed, Apr 16, 2003 at 02:05:15PM +0100, Stephen Henderson wrote: > Hi > Thanks for your help. Unfortunately this is not doing as I expected. Ia m > on Windows, affy version 1.1.1 and However, a glance at what is below makes me believe it does what I expect. In the example, ppsets is a 'list' of elements of class 'ProbeSet' (class?ProbeSet to know more about it, like where are the probe intensities (Would something like ppsets[[i]]@pm do what you expect ?)). > > R.version.string > [1] "R version 1.6.1, 2002-11-01" > > So > > > bigbatch2 > AffyBatch object > size of arrays=712x712 features (209917 kb) > cdf=HG-U133A (22283 affyids) > number of samples=53 > number of genes=22283 > annotation=hgu133a > notes= > > > EWS > [1] "209214_s_at" "210011_s_at" "210012_s_at" "210581_x_at" "211391_s_at" > [6] "211603_s_at" "211825_s_at" > > > ppsets<-probeset(bigbatch2, EWS) > > > ppsets > $"209214_s_at" > ProbeSet object: > id=209214_s_at > pm= 11 probes > > $"210011_s_at" > ProbeSet object: > id=210011_s_at > pm= 11 probes > > ... etc > > Where are the expected probe values? Do I need to change to the devel. > version? > > -----Original Message----- > From: Laurent Gautier [mailto:laurent@cbs.dtu.dk] > Sent: Tuesday, April 15, 2003 12:30 AM > To: Stephen Henderson > Cc: bioconductor@stat.math.ethz.ch > Subject: Re: [BioC] pm values > > 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 > > > ********************************************************************** > This email and any files transmitted with it are confidential and > intended solely for the use of the individual or entity to whom they > are addressed. If you have received this email in error please notify > the system manager (wibr.mail@ucl.ac.uk). All files are scanned for viruses. > ********************************************************************** > -- -------------------------------------------------------------- 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