[BioC] How to generate Spot Types File?

[Maciej Jończyk]

> Hi Maciej,
>    Thanks for the reply! If I didn't generate my dataset, but the
dataset is downloaded from GEO website, would the spot file be expected
to uploaded onto GEO?
>

Maybe not spot file itself, but some kind of file which describes spots'
positions, provides annotation, etc. From which you could make STF.
If you don't find it at GEO, look for it at website of
company/university which made the microarrys. Your files are in .gpr
format so information about
spots could be in .gal file associated with design of microarray.

Best Wishes,

> Thanks again,
> Casper

> > To: bioconductor at r-project.org; casshyr at hotmail.com
> > Subject: Re: [BioC] How to generate Spot Types File?
> > From: mjonczyk at biol.uw.edu.pl
> > CC: mjonczyk at biol.uw.edu.pl
> > Date: Mon, 21 Mar 2011 00:39:48 +0100
> >
> > > Date: Sat, 19 Mar 2011 19:20:38 -0700
> > > From: Casper Shyr <casshyr at hotmail.com>
> > > To: Bioconductor <bioconductor at stat.math.ethz.ch>
> > > Subject: [BioC] How to generate Spot Types File?
> > > Message-ID: <SNT121-W211EEED740F311D1A4CD53AEB20 at phx.gbl>
> > > Content-Type: text/plain
> > >
> > >
> > > Hello all,
> > > I am working with a series of expression arrays (in gpr formats
> > > generated by GenePix) to find DE genes. I wish to incorporate Spot
> > > Types File like in the demos in Limma manual, but I don't know how
to
> > > go about generating such file. To be more specific, how do I find
out
> > > what are all the possible types of spots in my dataset?
> >
> > Hi Casper,
> >
> > Spot Type File contains information which of spots are: positive
> > controls,
> > negative controls, print controls, blanks, cDNAs or oligos i.e.
probes
> > of interest, etc.
> >
> > Spots' status should be described in file supplied by arrays'
> > manufacturer.
> >
> > Best wishes,
> > Maciej
> >


Maciej Jończyk, MSc
Department of Plant Molecular Ecophysiology
Institute of Plant Experimental Biology
Faculty of Biology, University of Warsaw
02-096 Warszawa, Miecznikowa 1



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