[BioC] problems rma() with mouse exon affy data in exonmap package

[Ben Bolstad]

You can debate the wisdom or otherwise of using only a small number of
arrays on a philosophical or technical metric basis all you want. But
the error mentioned below is unrelated to the number of arrays used. In
fact the rma() function will happily process two or even a single array
without complaint. What Jim is alluding to with his question is that
rma() does not expect to be fed NA  PM probe intensities.

Best,

Ben 


On Wed, 2007-08-29 at 10:00 -0400, Naomi Altman wrote:
> Can you really use rma with just 2 arrays?
> 
> --Naomi
> 
> At 08:22 AM 8/29/2007, James W. MacDonald wrote:
> >Hi Bruce,
> >
> >bruce wrote:
> > > Dear all:
> > >
> > >    I currently faced this error when I tried the rma() with two sample
> > > of mouse exon affy data.
> > >
> > >    I appreciate get help from you!
> > >
> > >    Below is the whole process:
> > >
> > > /***********************************************************
> > >
> > > covdesc file's:
> > >
> > >               treatment
> > >
> > > Xu_1.CEL      a
> > >
> > > Xu_2.CEL      b
> > >
> > >
> > >> library(exonmap)
> > >
> > >> rawdata<-read.exon()
> > >
> > >> rawdata at cdfName<-"mouseexonpmcdf"
> >
> >What do you get if you type
> >
> >rawdata
> >
> >at an R prompt?
> >
> >How about
> >
> >sum(is.na(pm(rawdata)))
> >
> >?
> >
> >Best,
> >
> >Jim
> >
> >
> > >
> > >> rawdata.rma<-rma(rawdata)
> > >
> > > Background correcting
> > >
> > > Error in density.default(x, kernel = "epanechnikov", n = 2^14) :
> > >
> > > 'x' contains missing values
> > >
> > >> ls()
> > >
> > > [1] "rawdata"
> > >
> > >> sessionInfo()
> > >
> > > R version 2.5.0 (2007-04-23)
> > >
> > > i686-redhat-linux-gnu
> > >
> > >
> > > locale:
> > >
> > > LC_CTYPE=en_US.UTF8;LC_NUMERIC=C;LC_TIME=en_US.UTF8;
> > >
> > > LC_COLLATE=en_US.UTF8;LC_MONETARY=en_US.UTF8;
> > >
> > > 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" "tools" "stats" "graphics" "grDevices" "datasets"
> > >
> > > [7] "utils" "methods" "base"
> > >
> > >
> > > other attached packages:
> > >
> > > mouseexonpmcdf exonmap plier RMySQL DBI
> > >
> > > "1.1" "1.0.06" "1.6.0" "0.6-0" "0.2-3"
> > >
> > > RColorBrewer simpleaffy genefilter survival affy
> > >
> > > "1.0-1" "2.10.31" "1.14.1" "2.31" "1.14.2"
> > >
> > > affyio Biobase
> > >
> > > "1.4.1" "1.14.1"
> > >
> > > thanks
> > > bruce
> >
> >--
> >James W. MacDonald, M.S.
> >Biostatistician
> >Affymetrix and cDNA Microarray Core
> >University of Michigan Cancer Center
> >1500 E. Medical Center Drive
> >7410 CCGC
> >Ann Arbor MI 48109
> >734-647-5623
> >
> >_______________________________________________
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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
> 
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