> 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 > > 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]] > > > > ------------------------------ > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > End of Bioconductor Digest, Vol 97, Issue 20 > ******************************************** > > -- > This email was Anti Virus checked by Astaro Security Gateway. > http://www.astaro.com > Maciej Jo?czyk, 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

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]] > > > > > > > > ------------------------------ > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@r-project.org > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > > > > End of Bioconductor Digest, Vol 97, Issue 20 > > ******************************************** > > > > -- > > This email was Anti Virus checked by Astaro Security Gateway. > > http://www.astaro.com > > > > > Maciej Joñczyk, 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 > > > [[alternative HTML version deleted]]