Affy: pm and mm data from AffyID
2
0
Entering edit mode
@donald-dunbar-886
Last seen 10.2 years ago
Hello, sorry if this is a RFTM, but after reading the Affy vignette a few times, I can't find the answer, and I know it must be easy! I've loaded the Affy library and read my chips into bioconductor. I've no problem accessing PM and MM data by Index as shown in the vignette (4.1 Accessing PM and MM Data), however I can't see how to access the same data by AffyID. Any help would be appreciated, Donald ===================== Dr Donald Dunbar Bioinformatician Molecular Physiology Group Wilkie Building, Medical School, The University of Edinburgh, EH8 9AG t: +44 (0)131 651 1592 e: Donald.Dunbar@ed.ac.uk [[alternative HTML version deleted]]
affy affy • 1.2k views
ADD COMMENT
0
Entering edit mode
Ben Bolstad ★ 1.1k
@ben-bolstad-93
Last seen 10.2 years ago
Try using something like pm(Data,"1001_at") or pm(Data,c("1001_at","1002_at")) etc. Ben On Fri, 2004-08-20 at 07:58, Donald Dunbar wrote: > Hello, > sorry if this is a RFTM, but after reading the Affy vignette a few times, I > can't find the answer, and I know it must be easy! > I've loaded the Affy library and read my chips into bioconductor. I've no > problem accessing PM and MM data by Index as shown in the vignette (4.1 > Accessing PM and MM Data), however I can't see how to access the same data > by AffyID. > Any help would be appreciated, > Donald > > ===================== > Dr Donald Dunbar > Bioinformatician > Molecular Physiology Group > Wilkie Building, Medical School, > The University of Edinburgh, EH8 9AG > t: +44 (0)131 651 1592 > e: Donald.Dunbar@ed.ac.uk > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
ADD COMMENT
0
Entering edit mode
Thanks for that. Donald -----Original Message----- From: Ben Bolstad [mailto:bolstad@stat.berkeley.edu] Sent: 20 August 2004 16:06 To: Donald Dunbar Cc: bioconductor@stat.math.ethz.ch Subject: Re: [BioC] Affy: pm and mm data from AffyID Try using something like pm(Data,"1001_at") or pm(Data,c("1001_at","1002_at")) etc. Ben On Fri, 2004-08-20 at 07:58, Donald Dunbar wrote: > Hello, > sorry if this is a RFTM, but after reading the Affy vignette a few > times, I can't find the answer, and I know it must be easy! > I've loaded the Affy library and read my chips into bioconductor. I've > no problem accessing PM and MM data by Index as shown in the vignette > (4.1 Accessing PM and MM Data), however I can't see how to access the > same data by AffyID. > Any help would be appreciated, > Donald > > ===================== > Dr Donald Dunbar > Bioinformatician > Molecular Physiology Group > Wilkie Building, Medical School, > The University of Edinburgh, EH8 9AG > t: +44 (0)131 651 1592 > e: Donald.Dunbar@ed.ac.uk > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor -- Ben Bolstad <bolstad@stat.berkeley.edu> http://www.stat.berkeley.edu/~bolstad
ADD REPLY
0
Entering edit mode
@james-w-macdonald-5106
Last seen 2 days ago
United States
Use the pm() accessor function. pm(abatch, probeid) mm(abatch, probeid) HTH, Jim James W. MacDonald Affymetrix and cDNA Microarray Core University of Michigan Cancer Center 1500 E. Medical Center Drive 7410 CCGC Ann Arbor MI 48109 734-647-5623 >>> "Donald Dunbar" <donald.dunbar@ed.ac.uk> 08/20/04 10:58AM >>> Hello, sorry if this is a RFTM, but after reading the Affy vignette a few times, I can't find the answer, and I know it must be easy! I've loaded the Affy library and read my chips into bioconductor. I've no problem accessing PM and MM data by Index as shown in the vignette (4.1 Accessing PM and MM Data), however I can't see how to access the same data by AffyID. Any help would be appreciated, Donald ===================== Dr Donald Dunbar Bioinformatician Molecular Physiology Group Wilkie Building, Medical School, The University of Edinburgh, EH8 9AG t: +44 (0)131 651 1592 e: Donald.Dunbar@ed.ac.uk [[alternative HTML version deleted]] _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENT
0
Entering edit mode
An other option is to go through the class ProbeSet. mypps <- probeset(abatch, probeid) lapply(mypps, function(x) x@pm) lapply(mypps, function(x) x@mm) L. James MacDonald wrote: > Use the pm() accessor function. > > pm(abatch, probeid) > mm(abatch, probeid) > > > HTH, > > Jim > > > James W. MacDonald > Affymetrix and cDNA Microarray Core > University of Michigan Cancer Center > 1500 E. Medical Center Drive > 7410 CCGC > Ann Arbor MI 48109 > 734-647-5623 > > >>>>"Donald Dunbar" <donald.dunbar@ed.ac.uk> 08/20/04 10:58AM >>> > > Hello, > sorry if this is a RFTM, but after reading the Affy vignette a few > times, I > can't find the answer, and I know it must be easy! > I've loaded the Affy library and read my chips into bioconductor. I've > no > problem accessing PM and MM data by Index as shown in the vignette > (4.1 > Accessing PM and MM Data), however I can't see how to access the same > data > by AffyID. > Any help would be appreciated, > Donald > > ===================== > Dr Donald Dunbar > Bioinformatician > Molecular Physiology Group > Wilkie Building, Medical School, > The University of Edinburgh, EH8 9AG > t: +44 (0)131 651 1592 > e: Donald.Dunbar@ed.ac.uk > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor >
ADD REPLY

Login before adding your answer.

Traffic: 358 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6