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

Heike Pospisil pospisil at zbh.uni-hamburg.de
Fri Aug 22 18:43:31 CEST 2008


Hello again,

I have found the answer. The log ratios can be extracted using 

  con.kmean<-consensus(cluster.kmean,thres,draw=FALSE)
  con.kmean$data.draw

Best,
Heike

On Friday 22 August 2008 18:29, Heike Pospisil wrote:
> Hello 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_AD
>DRESS=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



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