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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="">
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<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="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
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