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

[Naomi Altman]

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