
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?

Thanks again,
Casper

> To: bioconductor@r-project.org; casshyr@hotmail.com
> Subject: Re: [BioC] How to generate Spot Types File?
> From: mjonczyk@biol.uw.edu.pl
> CC: mjonczyk@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@hotmail.com>
> > To: Bioconductor <bioconductor@stat.math.ethz.ch>
> > Subject: [BioC] How to generate Spot Types File?
> > Message-ID: <SNT121-W211EEED740F311D1A4CD53AEB20@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
> 
> >
> > Below is basically my codes of what I have so far, up to the part
> > before creating design matrix.
> > #load in target file
> > targets<-readTargets("spleen_target_file.txt")
> >
> > #Iignore anything < -50.
> > > f <- function(x) as.numeric(x$Flags -50.5)
> > RG <- read.maimages(targets, source="genepix", wt.fun=f)
> >
> > #Background correction
> > #It was reported that for assessing DE, use normexp with offset, get
> > better result than using simple background subtraction
> > RG_bc <- backgroundCorrect(RG, method="normexp", offset=50)
> >
> > #LOESS normalization
> > MA <- normalizeWithinArrays(RG_bc)
> >
> > Thanks!
> > Casper
> >
> > 	[[alternative HTML version deleted]]
> >
> >
> >
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> >
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> 
> 
> Maciej Jończyk, MSc
> Department of Plant Molecular Ecophysiology
> Institute of Plant Experimental Biology
> Faculty of Biology, University of Warsaw
> 02-096 Warszawa, Miecznikowa 1
> 
> 
> 
> ___________________________________
> NOCC, http://nocc.sourceforge.net
> 
> 
> 
 		 	   		  
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