Gene Screening.
1
0
Entering edit mode
@stephen-henderson-71
Last seen 7.7 years ago
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@cs.rug.nl] Sent: Thursday, October 02, 2003 5:54 PM To: James MacDonald Cc: bioconductor@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@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor ********************************************************************** This email and any files transmitted with it are confidentia...{{dropped}}
Microarray Cancer affy affycomp Microarray Cancer affy affycomp • 1.1k views
ADD COMMENT
0
Entering edit mode
@subramanian-karthikeyan-450
Last seen 10.3 years ago
Along the same lines, is there way a way I can do a two way anova to screen for signficantly regulated genes, before doing cluster or other analysis? The data is arranged so that the columns represent various levels of different treatments and controls and the rows correspond to the genes. Thanks, Karthi. Stephen Nyangoma <s.nyangoma@cs.rug.nl> To: James MacDonald <jmacdon@med.umich.edu> Sent by: cc: bioconductor@stat.math.ethz.ch bioconductor-bounces@stat.m Subject: [BioC] Gene Screening. ath.ethz.ch 2003-10-02 12:54 PM 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@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor _______________________________________________ Bioconductor mailing list Bioconductor@stat.math.ethz.ch https://www.stat.math.ethz.ch/mailman/listinfo/bioconductor
ADD COMMENT

Login before adding your answer.

Traffic: 621 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6