Question: maGnames
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gravatar for Clemi
17.1 years ago by
Clemi10
Clemi10 wrote:
This is a multi-part message in MIME format. ------=_NextPart_000_005D_01C28E70.7C3C6790 Content-Type: text/plain; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Dear collegues! I have started using R and the Bioconductor packages for microarray = analysis. How can I get the gene names of interesting points on the = maPlot?=20 I hope that you can help me... Yours sincerely ______________________________________________________________________ ___= _______________________ Clemens Achmueller Tyrolean Cancer Research Institute Innrain 66 6020 Innsbruck, Austria Tel:. +43 (512) 570 485-15=20 Fax: +43 (512) 570 485-44=20 www.tkfi.at ------=_NextPart_000_005D_01C28E70.7C3C6790 Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable <html><head> <meta http-equiv="3DContent-Type" content="3D"text/html;" =="" charset="3Diso-8859-1""> <meta content="3D"MSHTML" 5.50.4916.2300"="" name="3DGENERATOR"> <style></style> </head> <body bgcolor="3D#ffffff">
<font face="3DArial" size="3D2">Dear collegues!</font>
<font face="3DArial" size="3D2"></font> 
<font face="3DArial" size="3D2">I have started using R and the = Bioconductor=20 packages for microarray analysis. How can I get the gene names of = interesting=20 points on the maPlot? </font>
<font face="3DArial" size="3D2"></font> 
<font face="3DArial" size="3D2">I hope that you can help = me...</font>
<font face="3DArial" size="3D2"></font> 
<font face="3DArial" size="3D2">Yours sincerely</font>
<font face="3DArial" size="3D2"></font> 
<font face="3DArial" =="" size="3D2">

_____________________________________________________________ ___= ________________________________
Clemens=20 Achmueller
Tyrolean Cancer Research Institute
Innrain 66
6020=20 Innsbruck, Austria
 
Tel:. +43  (512) 570 485-15
Fax: +43  (512) 570 = 485-44
 
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microarray cancer • 534 views
ADD COMMENTlink modified 17.1 years ago by Chapman, Scott PI, Indooroopilly10 • written 17.1 years ago by Clemi10
Answer: maGnames
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gravatar for Chapman, Scott PI, Indooroopilly
17.1 years ago by
This message is in MIME format. Since your mail reader does not understand this format, some or all of this message may not be legible. ------_=_NextPart_001_01C28F5F.443910B4 Content-Type: text/plain; charset="iso-8859-1" Clemens, It depends on whether you want to identify "interesting genes" by a statistical/cutoff method (there are several available in BioConductor and in other packages) or by picking them from a graph using the mouse. If you run the last example in the maPlot helpfile, it uses maTop as a text.func argument within maPlot to highlight genes in the top 1% of the tails for array 1 in swirl. You can list the highlighted gene names by subsetting the gene labels in swirl using the same argument from the example plot: maLabels(maGnames(swirl))[maTop(maM(swirl)[,1],h=0.01,l=0.01)] The text.func argument can be replaced by numerous alternatives. If you want to pick genes using the mouse (in Windows: left clicks to choose, right to click to stop) & save to an object you could do the following : selected.points <- identify(maA(swirl)[,1],maM(swirl)[,1],labels=maLabels(maGnames(swirl) )) selected.genes <- maLabels(maGnames(swirl))[selected.points] cheers, scott c. Dr. Scott Chapman, Crop Adaptation Scientist CSIRO Plant Industry, Australia -----Original Message----- From: Clemi [mailto:clemens.achmueller@uibk.ac.at] Sent: Monday, 18 November 2002 4:35 AM To: bioconductor@stat.math.ethz.ch Subject: [BioC] maGnames Dear collegues! I have started using R and the Bioconductor packages for microarray analysis. How can I get the gene names of interesting points on the maPlot? I hope that you can help me... Yours sincerely ______________________________________________________________________ ______ ____________________ Clemens Achmueller Tyrolean Cancer Research Institute Innrain 66 6020 Innsbruck, Austria Tel:. +43 (512) 570 485-15 Fax: +43 (512) 570 485-44 www.tkfi.at <http: www.tkfi.at=""> ------_=_NextPart_001_01C28F5F.443910B4 Content-Type: text/html; charset="iso-8859-1" <html><head> <meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"> <meta content="MSHTML 5.50.4616.200" name="GENERATOR"> <style></style> </head> <body bgcolor="#ffffff">
<font face="Arial" color="#0000ff" size="2">Clemens,</font>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">It depends on whether you want to identify "interesting genes" by a statistical/cutoff method (there are several available in BioConductor and in other packages) or by picking them from a graph using the mouse. If you run the last example in the maPlot helpfile, it uses maTop as a text.func argument within maPlot to highlight genes in the top 1% of the tails for array 1 in swirl. You can list the highlighted gene names by subsetting the gene labels in swirl using the same argument from the example plot:</font>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">maLabels(maGnames(swirl))[maTop(maM(swirl)[,1],h=0.01,l=0.01)]< /FONT>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">The text.func argument can be replaced by numerous alternatives.</font>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">If you want to pick genes using the mouse (in Windows: left clicks to choose, right to click to stop) & save to an object you could do the following :</font>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">selected.points <- identify(maA(swirl)[,1],maM(swirl)[,1],labels=maLabels(maGnames(swirl) ))
<font face="Arial" color="#0000ff" size="2">selected.genes <- </font>maLabels(maGnames(swirl))[<font face="Arial" color="#0000ff" size="2">selected.points</font>]</font>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">cheers,</font>
<font face="Arial" color="#0000ff" size="2"></font> 
<font face="Arial" color="#0000ff" size="2">scott c.</font>
<font face="Arial" color="#0000ff" size="2">

<font size="2">Dr. Scott Chapman, Crop Adaptation Scientist
CSIRO Plant Industry, Australia
</font>

</font>
<font face="Tahoma" size="2">-----Original Message-----
From: Clemi [mailto:clemens.achmueller@uibk.ac.at]
Sent: Monday, 18 November 2002 4:35 AM
To: bioconductor@stat.math.ethz.ch
Subject: [BioC] maGnames

</font>
<font face="Arial" size="2">Dear collegues!</font>
<font face="Arial" size="2"></font> 
<font face="Arial" size="2">I have started using R and the Bioconductor packages for microarray analysis. How can I get the gene names of interesting points on the maPlot? </font>
<font face="Arial" size="2"></font> 
<font face="Arial" size="2">I hope that you can help me...</font>
<font face="Arial" size="2"></font> 
<font face="Arial" size="2">Yours sincerely</font>
<font face="Arial" size="2"></font> 
<font face="Arial" size="2">

___________________________________________________________ _____________________________________
Clemens Achmueller
Tyrolean Cancer Research Institute
Innrain 66
6020 Innsbruck, Austria
 
Tel:. +43  (512) 570 485-15
Fax: +43  (512) 570 485-44
 
</html> ------_=_NextPart_001_01C28F5F.443910B4--
ADD COMMENTlink written 17.1 years ago by Chapman, Scott PI, Indooroopilly10
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