[BioC] RE: mva.pairs

[Stephen Henderson]

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 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:
>Try 
>>mva.pairs(exprs(eset))
>
>-----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
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
>
>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
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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
****************************************************************************
*************** 


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