[BioC] Re: Single channel normalization
thorne at wehi.EDU.AU
Wed Sep 10 15:29:22 MEST 2003
We have just added to limma some functions and documentation for doing
single-channel normalization. Limma is an R package that has been included
in the Bioconductor release package. Gordon Smyth is the maintainer
for limma and the package is frequently updated. You should go to
http://bioinf.wehi.edu.au/limma/ for the latest release which now includes
the single-channel(sc) normalization functionality and function for
plotting the single-channel densities.
This latest release has also just been posted to Bioconductor to the
Developmental Package of limma at http://www.bioconductor.org/ and will be
available there shortly.
In R use help.start() and go to packages...limma...Accommpanying
documentation...usersguide (in .html or .pdf)
Section 14 of the usersguide is on single-channel normalization for
two-color arrays. This gives an example of normalizing the
single-channels of the ApoAI data set which is part of sma.
See also the help examples for the function plotDensities,
normalizeWithinArrays, and normalizeBetweenArrays. Some of these
examples are given below.
# just bkg corr
MA.n <- MA.RG(mouse.data) # no normalization
MA.q <- normalizeBetweenArrays(MA.p, method = "q") # quantile norm
G.q <- normalizeBetweenArrays(RG.MA(MA.n)$G,method="q") # only green sc's
# takes a matrix
tmp<-cbind(RG.MA(MA.n)$R,RG.MA(MA.n)$G)[,c(1,3,8,9,12)] # select sc's
tmp.q <- normalizeBetweenArrays(tmp, method = "q") # takes a matrix
MA.p <- normalizeWithinArrays(MA.n, mouse.setup) # default p-loess
MA.pq <- normalizeBetweenArrays(MA.p, method = "q") # pq norm
MA.MpAq <- normalizeBetweenArrays(MA.p, method = "Aq") # MpAq norm
# Yang & Thorne 03
plotDensities(MA.n) # default
plotDensities(MA.n,arrays=c(1:6), # same as default
plotDensities(MA.n,arrays=NULL,groups=NULL, # diff cols
plotDensities(MA.n,singlechannels=c(1,2,7)) # indexing sc's
plotDensities(MA.n,singlechannels=c(1,2,7), # diff cols
plotDensities(MA.n,singlechannels=c(1,2,7), # groups=2
col=c("pink","purple","blue")) # col too long
plotDensities(MA.n,singlechannels=c(1,2,7), # controlling
groups=c(1,2,3),col=c("pink","purple","blue")) # col and groups
# All single-channels, three groups (ctl,tmt,reference), three colors.
# Densities after single-channel MpAq (preferred) normalization.
* * Natalie Thorne, Phd Student.
* * Genetics and Bioinformatics Division,
* The Walter And Eliza Hall Institute
* * Of Medical Research (WEHI).
* * PO Royal Melbourne Hospital, 3050
* * PH: +61 3 9345 2631
* Fax: +61 3 9347 0852
* * URL http://bioinf.wehi.edu.au
* * Mathematics and Statistics Department,
* The University of Melbourne
* * Fax: +61 3 9344 4599
* CRC for discovery of genes for common
* * human diseases.
* * Email : thorne at wehi.edu.au
On Tue, 9 Sep 2003, cmprobst wrote:
> Hi, Natalie
> I would like to ask you some question about single channel normalization, mainly the how-to.
> I am asking you for suggestion in how to plot the density functions as
was done in the paper with Jean Yang.
> And also, if it is possible to apply the quantiles.normalization (and if
yes, how) in a matrix of m spots per n hybs.
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