[BioC] RE: mva.pairs

Stephen Henderson s.henderson at ucl.ac.uk
Thu Aug 14 15:35:59 MEST 2003

ps to make it quicker you may also wish to only sample some genes (not

>samp<- sample(1:22000, 1000, replace=F)

>mva.pairs(exprs(eset[samp,Sel]), log.it=F)

-----Original Message-----
From: Anna Gustafsson [mailto:annag at 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:
>-----Original Message-----
>From: Anna Gustafsson [mailto:annag at biotech.kth.se] 
>Sent: Thursday, August 14, 2003 2:13 PM
>To: bioconductor at 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
>(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)
>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: Roslagsvägen 30B
>Bioconductor mailing list
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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: Roslagsvägen 30B

This email and any files transmitted with it are confidentia...{{dropped}}

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