[BioC] maGnames
Chapman, Scott (PI, Indooroopilly)
Scott.Chapman@csiro.au
Tue, 19 Nov 2002 10:04:44 +1000
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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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<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2>Clemens,</FONT></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><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></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2>maLabels(maGnames(swirl))[maTop(maM(swirl)[,1],h=0.01,l=0.01)]</FONT></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff size=2>The
text.func argument can be replaced by numerous alternatives.</FONT></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><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></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2>selected.points <-
identify(maA(swirl)[,1],maM(swirl)[,1],labels=maLabels(maGnames(swirl)))<BR><SPAN
class=738203022-18112002><FONT face=Arial color=#0000ff size=2>selected.genes
<- </FONT></SPAN>maLabels(maGnames(swirl))[<SPAN
class=738203022-18112002><FONT face=Arial color=#0000ff
size=2>selected.points</FONT></SPAN>]</FONT></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2>cheers,</FONT></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff
size=2></FONT></SPAN> </DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff size=2>scott
c.</FONT></SPAN></DIV>
<DIV><SPAN class=738203022-18112002><FONT face=Arial color=#0000ff size=2>
<P><FONT size=2>Dr. Scott Chapman, Crop Adaptation Scientist<BR>CSIRO Plant
Industry, Australia<BR></FONT><BR></P></DIV></FONT></SPAN>
<BLOCKQUOTE dir=ltr
style="PADDING-LEFT: 5px; MARGIN-LEFT: 5px; BORDER-LEFT: #0000ff 2px solid; MARGIN-RIGHT: 0px">
<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B> Clemi
[mailto:clemens.achmueller@uibk.ac.at]<BR><B>Sent:</B> Monday, 18 November
2002 4:35 AM<BR><B>To:</B> bioconductor@stat.math.ethz.ch<BR><B>Subject:</B>
[BioC] maGnames<BR><BR></FONT></DIV>
<DIV><FONT face=Arial size=2>Dear collegues!</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><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></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I hope that you can help me...</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Yours sincerely</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV><FONT face=Arial size=2>
<DIV><BR>________________________________________________________________________________________________<BR>Clemens
Achmueller<BR>Tyrolean Cancer Research Institute<BR>Innrain 66<BR>6020
Innsbruck, Austria</DIV>
<DIV> </DIV>
<DIV>Tel:. +43 (512) 570 485-15 <BR>Fax: +43 (512) 570 485-44
</DIV>
<DIV> </DIV>
<DIV><A
href="http://www.tkfi.at">www.tkfi.at</A></FONT></DIV></BLOCKQUOTE></BODY></HTML>
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