[BioC] Gene Screening.

[Stephen Henderson]

It depends what you are working with if you are looking at data in an
exprSet then have a look at the esApply function

>?esApply

>fun<-function(x){ mean(x)}

>level<-esApply(eset, 1 fun)

> wh<- which(level> whatever)

etc...etc..

-----Original Message-----
From: Stephen Nyangoma [mailto:S.Nyangoma at cs.rug.nl] 
Sent: Thursday, October 02, 2003 5:54 PM
To: James MacDonald
Cc: bioconductor at stat.math.ethz.ch
Subject: [BioC] Gene Screening.

Hi all,
Is there a simple way in Bioconductor to screen the genes so that one
considers only "well expressed" genes?

Thanks. Steve.


On Thu, 2003-10-02 at 15:52, James MacDonald wrote:
> It's probably not on your end. I don't think affy 1.3.14 and R-1.8.0 are
> fully compatible yet. R-1.8.0 just recently went into feature freeze, so
> I think it will take a little bit for the affy maintainers to get
> everything squared away.
> 
> Jim
> 
> 
> 
> James W. MacDonald
> Affymetrix and cDNA Microarray Core
> University of Michigan Cancer Center
> 1500 E. Medical Center Drive
> 7410 CCGC
> Ann Arbor MI 48109
> 734-647-5623
> 
> >>> "Nicholas Lewin-Koh" <nikko at hailmail.net> 10/02/03 03:34AM >>>
> Hi,
> Not sure if this is on my end or not. Using todays R-1.8.0 beta
> release
> and RH linux 9.0:
> 
> > getBioC(relLevel = "devel",destdir="test/testlibs")
>     .......
> 
> [1] "Attempting to download affy from
> http://www.bioconductor.org/repository/devel/package/Source"
> [1] "Download complete."
> [1] "Installing affy"
> * Installing *source* package 'affy' ...
> creating cache ./config.cache
> checking how to run the C preprocessor... cc -E
> checking for main in -lz... yes
> checking for zlib.h... yes
> checking if zlib version >= 1.1.3... yes
> updating cache ./config.cache
> creating ./config.status
> creating src/Makevars
> ** libs
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c chipbackground.c -o
> chipbackground.o
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c getall_locations.c -o
> getall_locations.o
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c qnorm.c -o qnorm.o
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c read_abatch.c -o
> read_abatch.o
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c read_cdffile.c -o
> read_cdffile.o
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c rma2.c -o rma2.o
> gcc --Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c rma_background2.c -o
> rma_background2.o
> gcc -Itest/lib/R/include -DHAVE_ZLIB=1  -I/usr/local/include
> -D__NO_MATH_INLINES -mieee-fp  -fPIC  -g -O2 -c rma_common.c -o
> rma_common.o
> gcc -shared -L/usr/local/lib -o affy.so chipbackground.o
> getall_locations.o qnorm.o read_abatch.o read_cdffile.o rma2.o
> rma_background2.o rma_common.o -lz   
> -L/test/lib/R/bin -lR
> ** R
> ** data
> ** demo
> ** inst
> ** save image
> Welcome to Bioconductor
>          Vignettes contain introductory material.  To view,
>          simply type: openVignette()
>          For details on reading vignettes, see
>          the openVignette help page.
> [1] TRUE
> [1] TRUE
> [1] TRUE
> [1] "Cdf"
> [1] "name.levels"
> [1] "name.levels"
> [1] "name.levels<-"
> [1] "name.levels<-"
> [1] "pbase"
> [1] "pbase"
> [1] "pbase<-"
> [1] "pbase<-"
> [1] "pbase.levels"
> [1] "pbase.levels"
> [1] "pbase.levels<-"
> [1] "pbase.levels<-"
> [1] "tbase"
> [1] "tbase"
> [1] "tbase<-"
> [1] "tbase<-"
> [1] "tbase.levels"
> [1] "tbase.levels"
> [1] "tbase.levels<-"
> [1] "tbase.levels<-"
> [1] "atom"
> [1] "atom"
> [1] "atom<-"
> [1] "atom<-"
> [1] "probeNames"
> [1] "probeNames"
> [1] "probeNames<-"
> [1] "probeNames<-"
> [1] "show"
> [1] "AffyBatch"
> [1] "intensity"
> [1] "intensity"
> [1] "intensity<-"
> [1] "intensity<-"
> [1] "length"
> [1] "ncol"
> [1] "ncol"
> [1] "nrow"
> [1] "nrow"
> [1] "getCdfInfo"
> [1] "getCdfInfo"
> Error in getMethodsForDispatch(f, fdef) : Trying to get slot
> ".Methods"
> from an
> object whose class ("genericMethods") is not defined
> Execution halted
> test/lib/R/bin/INSTALL: line 1: 15051 Broken pipe             cat
> "test/testlibs/affy/R/affy"
> ERROR: execution of package source for 'affy' failed
> ** Removing 'test/testlibs/affy'
> Warning message:
> Installation of package affy had non-zero exit status in:
> installPkg(fileName, pkg, pkgVer, type, lib, repEntry, versForce)
> [1] "Attempting to download affycomp from
> http://www.bioconductor.org/repository/devel/package/Source"
>  
> 
> Note if some of the paths look funny I had to take them out becuase of
> company security.
> 
> Nicholas
> 
> _______________________________________________
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> 
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