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

[bruce]

Hi Jim,Ben and Naomi:
        
    Thanks for your help. The rawdata and sum of it's missing value
information follows below:

> rawdata

AffyBatch object

size of arrays=2560x2560 features (8 kb)

cdf=mouseexonpmcdf (1201338 affyids)

number of samples=2

number of genes=1201338

annotation=moex10stv1

notes=

> sum(is.na(pm(rawdata)))

[1] 17940

> summary(exprs(rawdata))

Xu_1.CEL 	Xu_2.CEL

Min. : 19.0 	Min. : 19.0

1st Qu.: 33.0 	1st Qu.: 34.0

Median : 50.0	Median : 57.0

Mean : 263.7 	Mean : 287.5

3rd Qu.: 114.0 	3rd Qu.: 140.0

Max. :23585.0 	Max. :23777.0

NA's :26215.0

Sincerely
Bruce

On Wed, 2007-08-29 at 07:40 -0700, Ben Bolstad wrote:
> 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
> > >
> > >_______________________________________________
> > >Bioconductor mailing list
> > >Bioconductor at stat.math.ethz.ch
> > >https://stat.ethz.ch/mailman/listinfo/bioconductor
> > >Search the archives: 
> > >http://news.gmane.org/gmane.science.biology.informatics.conductor
> > 
> > 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
> > 
> > _______________________________________________
> > Bioconductor mailing list
> > Bioconductor at stat.math.ethz.ch
> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor
> 
> 
-- 
Guangzhou Institute of Biomedicine and Health,Chinese Academy of
Sciences
Öйú¿ÆѧԺ¹ãÖÝÉúÎïÒ½Ò©Ó뽡¿µÑо¿Ôº
http://www.gibh.ac.cn
Email:chen_zhaoming at gibh.ac.cn,neamee at gmail.com
Office:020-32290510
Mobile:13480217655