[BioC] Gene Screening.
Subramanian Karthikeyan
Subramanian_Karthikeyan at hc-sc.gc.ca
Thu Oct 2 16:45:20 MEST 2003
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 at cs.rug.nl> To: James MacDonald <jmacdon at med.umich.edu>
Sent by: cc: bioconductor at stat.math.ethz.ch
bioconductor-bounces at 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 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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