[BioC] Compare results from different analysis (Affymetrix)

[Sean Davis]

On Tuesday 12 December 2006 05:14, Ingrid H. G. Østensen wrote:
> Hi
>
> More information:
> 1,50 GB RAM
>
> > sessionInfo()
>
> R version 2.4.0 (2006-10-03)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=Norwegian (Bokmål)_Norway.1252;LC_CTYPE=Norwegian
> (Bokmål)_Norway.1252;LC_MONETARY=Norwegian
> (Bokmål)_Norway.1252;LC_NUMERIC=C;LC_TIME=Norwegian (Bokmål)_Norway.1252
>
> attached base packages:
> [1] "methods"   "stats"     "graphics"  "grDevices" "utils"     "datasets"
> [7] "base"
>
> From the runing of the script:
> > library(limma)
> > library(affyQCReport)
>
> Loading required package: Biobase
> Loading required package: tools
>
> Welcome to Bioconductor
>
>     Vignettes contain introductory material. To view, type
>     'openVignette()' or start with 'help(Biobase)'. For details
>     on reading vignettes, see the openVignette help page.
>
> Loading required package: affy
> Loading required package: affyio
> Loading required package: simpleaffy
> Loading required package: genefilter
> Loading required package: survival
> Loading required package: splines
> Welcome to 'affyQCReport' V 1.6-1
> Further information available at: www.bifix.org
>       mailto: craig.parman at bifix.org
>
> > library(RColorBrewer)
> > library(xtable)
> > library(simpleaffy)
> > memory.limit(4000)
>
> NULL
>
> > dataSet <- read.affy()

Thanks, Ingrid, for the details.  As Jim already suggested, using justRMA 
should probably allow you to load all of your arrays.  You will get back an 
ExpressionSet which you can then use for further analyses.  Normalizing and 
analyzing all your data simultaneously has significant advantages over the 
piecemeal approach.

Sean