[BioC] Compare results from different analysis (Affymetrix)

[Naomi Altman]

If I have so many arrays that I need to use 
justRMA to normalize, I do the QC in small 
batches first.  Using cross-array comparisons for 
QC makes most sense when you expect the arrays to 
be similar, so I read in all the replicates for 
one condition.  But for statistical differential 
expression analysis, the arrays should be normalized all together.

--Naomi

At 02:56 AM 12/13/2006, Ingrid H. G. Østensen wrote:
>Hi
>
>I usually do a quality control of the data 
>before I turn the data set into an 
>ExpressionSet. If I use justRMA, how can I then 
>quality control the data to see if any array 
>should be removed? Will it not be difficult if 
>all the arrays are corrected as they are read into the program?
>
>Regards,
>Ingrid
>
>
>
>-----Original Message-----
>From: Sean Davis [mailto:sdavis2 at mail.nih.gov]
>Sent: Tue 12/12/2006 12:39
>To: Ingrid H. G. Østensen
>Cc: bioconductor at stat.math.ethz.ch
>Subject: Re: [BioC] Compare results from different analysis (Affymetrix)
>
>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
>
>
>         [[alternative HTML version deleted]]
>
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Naomi S. Altman                                814-865-3791 (voice)
Associate Professor
Dept. of Statistics                              814-863-7114 (fax)
Penn State University                         814-865-1348 (Statistics)
University Park, PA 16802-2111