[BioC] How to generate Spot Types File?

[Maciej Jończyk]

> 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
>
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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



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