[BioC] Writing MAList to file (limma)

[michael watson (IAH-C)]

Hi Joel

Depending on how you read your data in, the genes slot of your Rglist
should be full of probe names.  If it's not then you can set it by:

RG$genes <- readGAL(...)

Then, when you create and MAList from that RGList, the genes slot should
be transferred over, so:

out<-Cbind(MA$genes, MA$M)
write.table(out,...)

It's very important to realise that R and bioconductor, in many
functions, relies on the fact that data in different files are in the
same order - so if I read 12 gpr files in, it assumes they are ain
Block,Row,Column order, and if they are not all in the same order, it
doesn't do any cross-referencing.

Hope that helps

Mick

-----Original Message-----
From: Malard, Joel M [mailto:JM.Malard at pnl.gov] 
Sent: 12 October 2004 00:59
To: bioconductor at stat.math.ethz.ch
Subject: [BioC] Writing MAList to file (limma)


Hi,

Is there a natural way to write normalized MA values along with the
correct probe names? 
One can write the M and A values as tables but the row indices need not
match 
the order of the probe names in the CEL files.

Thank you for your help and my apologies if this is a trite question,  

Joel M. Malard, Ph.D.
Scientist IV
Pacific Northwest National Laboratory
Battelle Boulevard, PO Box 999
Mail Stop K1-85
Richland, WA 99352

"I love the audacity of those who have everything to loose from it; the
moderation of those who have nothing to gain from it." Rostand, Jean
(1894-1977)



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