[BioC] How to extract log ratios from two color arrays

[Heike Pospisil]

Hallo BioC list,

I am analysing 38 two color arrays for a time course experiment with dye swap 
(5 time points). I have used maanova for normalisation and macluster() for 
clustering (see code below). 

Now, I am wondering how to extract the log ratios (R/G) for each gene for each 
time point. The consensus() function plots these values, and I would like to 
know how to get them.

Thanks a lot,
Heike


#########################################################
maanova.raw <- read.madata("maanovafile.txt", 
                           designfile="designfile.txt",
                           metarow=1, metacol=2, col=3, row=4,              
                           probeid=5,intensity=7,
                           arrayType='twoColor',
                           log.trans=T, spotflag=T)

my.data<-transform(maanova.raw,method="rlowess")

fit.fix<-fitmaanova(my.data,formula=~Dye+Array+Sample)

cluster.kmean<-macluster(fit.fix,term="Sample",                        
                         idx.gene=idx.fix$idx.all,
                         what="gene",method="kmean",
                         kmean.ngroups=8,n.perm=100)

consensus(cluster.kmean,0.8)

> sessionInfo()
R version 2.7.0 (2008-04-22)
i686-pc-linux-gnu

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
 [1] splines   tcltk     tools     stats     graphics  grDevices utils
 [8] datasets  methods   base

other attached packages:
 [1] hgu133a.db_2.2.0    maanova_1.8.1       GOstats_2.6.0
 [4] Category_2.6.0      genefilter_1.20.0   survival_2.34-1
 [7] RBGL_1.16.0         graph_1.18.1        annotate_1.18.0
[10] xtable_1.5-1        org.Hs.eg.db_2.2.0  goProfiles_1.2.0
[13] GO.db_2.2.0         AnnotationDbi_1.2.2 RSQLite_0.6-9
[16] DBI_0.2-4           marray_1.12.0       tkWidgets_1.14.0
[19] DynDoc_1.14.0       widgetTools_1.12.0  gplots_2.3.2
[22] gdata_2.2.0         gtools_2.3.0        DNAcopy_1.10.0
[25] biomaRt_1.10.0      XML_1.9-0           RCurl_0.8-0
[28] limma_2.12.0        Biobase_2.0.1

loaded via a namespace (and not attached):
[1] cluster_1.11.10

-- 
Dr. Heike Pospisil      | pospisil at zbh.uni-hamburg.de
University of Hamburg   | Center for Bioinformatics 
Bundesstrasse 43        | 20146 Hamburg, Germany 
phone:+49-40-42838-7303 | fax: +49-40-42838-7312