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Heike Pospisil
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310
@heike-pospisil-1097
Last seen 10.2 years ago
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_N
AME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTI
FICATION=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