Entering edit mode
Stephen Henderson
★
1.0k
@stephen-henderson-71
Last seen 7.7 years ago
OK try something like
>Sel<-c(1,4,5,6)
or
>Sel<- 1:3
then
>mva.pairs(exprs(eset[,Sel]))
REM if you are using rma or similar to put in log.it=F (so the results
are
not logged again).
e.g.
>mva.pairs(exprs(eset[,Sel]), log.it=F)
If there's a wrong un in there you'll see aline of skewed or highly
spread
scatters.
-----Original Message-----
From: Anna Gustafsson [mailto:annag@biotech.kth.se]
Sent: Thursday, August 14, 2003 2:26 PM
To: Stephen Henderson
Subject: mva.pairs
OK! Seems to generate plots. But how can I decide which chips to be
compared
to each other? I have 7 chips in this particular test experiment and
want to
be able to test each against all others more or less. Is it "doable"
:)?
Thanks for helping out!
// Anna :o)
At 14:14 2003-08-14 +0100, you wrote:
>Try
>>mva.pairs(exprs(eset))
>
>-----Original Message-----
>From: Anna Gustafsson [mailto:annag@biotech.kth.se]
>Sent: Thursday, August 14, 2003 2:13 PM
>To: bioconductor@stat.math.ethz.ch
>Subject: [BioC] (no subject)
>
>Dear all,
>
>Unfortunately - more questions:
>I wonder how to use mva.pairs to plot 2 replicate slides from an
"eset"
>object of background corrected, normalized, pm corrected and
summarized
data
>(i.e rma output).
>
>I can only find a vignette describing plots from only normalized, non
>summarized (16 individual expression measures / gene plotted) and I
do not
>understand how to transfer that information to work for my data in
the
>"eset" format..... :(
>
>With hopes on help!
>
>// Anna :o)
>
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>Anna Gustafsson
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>Royal Institute of Technology
>AlbaNova University Center
>Stockholm Center for Physics, Astronomy and Biotechnology
>Department of Molecular Biotechnology
>106 91 Stockholm, Sweden
>
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Anna Gustafsson
Royal Institute of Technology
AlbaNova University Center
Stockholm Center for Physics, Astronomy and Biotechnology
Department of Molecular Biotechnology
106 91 Stockholm, Sweden
Phone (office): +46 8 553 783 41
Fax: + 46 8 553 784 81
Visiting adress: Roslagstullsbacken 21, Floor 3
Delivery adress: Roslagsv?gen 30B
**********************************************************************
******
***************
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This email and any files transmitted with it are
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