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

[James W. MacDonald]

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