[BioC] Re: time serie data

[Nicholas Lewin-Koh]

> Message: 5
> Date: Wed, 1 Oct 2003 11:50:17 -0400
> From: Mike Schaffer <mschaff at bu.edu>
> Subject: [BioC] Time series data
> To: bioconductor at stat.math.ethz.ch
> Message-ID: <F4670CC1-F426-11D7-87BC-000393677AD6 at bu.edu>
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> 
> Is there a package capable of visualizing time series data a la Gene 
> Spring?  How about for normalizing replicate time series data points?
> 
> --
> Mike
> 
Hi,
Just to follow up Vince's note, have had very good results using Rggobi
to visualize time series. Just use the time points as colums and the
genes as rows and out it into a parallel coordinates plot view. If you
hve covariates code them as extra colums and they will come up as
categorical varibles in ggobi.

Nicholas 

> 
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> 
> Message: 7
> Date: Wed, 1 Oct 2003 12:08:20 -0400 (EDT)
> From: Vincent Carey 525-2265 <stvjc at channing.harvard.edu>
> Subject: Re: [BioC] Time series data
> To: Mike Schaffer <mschaff at bu.edu>
> Cc: bioconductor at stat.math.ethz.ch
> Message-ID:
> 	<Pine.GSO.4.40.0310011200460.19162-100000 at capecod.bwh.harvard.edu>
> Content-Type: TEXT/PLAIN; charset=US-ASCII
> 
> 
> > Is there a package capable of visualizing time series data a la Gene
> > Spring?  How about for normalizing replicate time series data points?
> 
> I don't know what Gene Spring does, can you provide an example?
> 
> The Iyer517 data package is an example of a time course
> experiment carried out with cDNA arrays.  This can be
> visualized using the parcoord function of MASS (once
> you convert the exprSet data to a matrix) and interactive
> brushable graphics of the time series can be created
> using ggobi/Rggobi.
> 
> If we extended the exprSet class to timedExprSet, where
> there was a standard encoding of the time course, a plot
> method which used one of these methods of visualization
> would be straightforward.  Consider this an RFC -- do we need
> it, if so what should it look like?  Or is there something
> in bioc that I am forgetting about?
> 
> 
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