Hi Morgan, It worked with the updated R version. Thanks On Tue, Oct 26, 2010 at 1:30 PM, Martin Morgan <mtmorgan@fhcrc.org> wrote: > On 10/26/2010 09:45 AM, viritha kaza wrote: > > > > Hi Morgan, > > The sessionInfo was > > R version 2.10.0 (2009-10-26) > > i386-pc-mingw32 > > locale: > > [1] LC_COLLATE=English_United States.1252 > > [2] LC_CTYPE=English_United States.1252 > > [3] LC_MONETARY=English_United States.1252 > > [4] LC_NUMERIC=C > > [5] LC_TIME=English_United States.1252 > > attached base packages: > > [1] stats graphics grDevices utils datasets methods base > > loaded via a namespace (and not attached): > > [1] tools_2.10.0 > > you will want to update to the current released version of R, and to > install the current version of the affy package > > source('http://bioconductor.org/biocLite.R') > biocLite('affy') > > Provide sessionInfo() after attaching the affy package; I see something > like > > > sessionInfo() > R version 2.12.0 Patched (2010-10-17 r53355) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=en_US.UTF-8 LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] affy_1.28.0 Biobase_2.10.0 > > loaded via a namespace (and not attached): > [1] affyio_1.18.0 preprocessCore_1.12.0 tools_2.12.0 > > and provide a simple and reproducible example to illustrate the problem > that you are having. For instance, I do not have a problem with > > > m = matrix(rnorm(100000 * 100), nrow=100000, ncol=100) > > n = normalize.loess(m) > > Here > > exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = "\t", > row.names = 1, as.is = TRUE)) > > it might be that you do not have a numeric matrix or other oddity; > confirm that it is as you expect. > > Martin > > > > > > -Viritha > > > > > > > > On Tue, Oct 26, 2010 at 11:57 AM, Martin Morgan <mtmorgan@fhcrc.org> > <mailto:mtmorgan@fhcrc.org>> wrote: > > > > On 10/26/2010 08:10 AM, viritha kaza wrote: > > > Hi, > > > Let me explain the issue clearly.I have taken the agilent 4x44 > > array series > > > matrix file from geo and removed the above information except the > > expression > > > data with ids in row 1 and column1 with GSMs.I am trying to > > normalise it > > > with cyclic loess method. > > > > > > exprs <- as.matrix(read.table("GSE__.txt[1]", header = TRUE,sep = > > "\t", > > > row.names = 1, as.is <http: as.is=""/> = TRUE)) > > > > > > then to normlize i used > > > > > > normalize.loess(exprs,epsilon=1,log.it > > <http: log.it=""/>=F,span=0.4,maxit=2) > > > > > > when I am doing this it doesnot show any error but my system shuts > > down.I > > > guess this is because it is too much of processing.So is my method > > correct > > > or should I have to break it and analyze if so how do I do it? > > > > Hi Viritha -- > > > > it is unlikely a problem of too much data but rather version > > incompatibility in installed packages. Tell us > > > > sessionInfo() > > > > after following > > > > > http://bioconductor.org/install/index.html#update-bioconductor- packages > > > > Since 'exprs' is just a matrix provide us with a reproducible example > > using random data, exprs = matrix(<...>) where <...> is sufficient to > > generate the problem on your system. > > > > Martin > > > > > > > > I hope it is clear now. > > > > > > Thank you in advance, > > > > > > Viritha > > > > > > [[alternative HTML version deleted]] > > > > > > _______________________________________________ > > > Bioconductor mailing list > > > Bioconductor@stat.math.ethz.ch <mailto:> Bioconductor@stat.math.ethz.ch> > > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > > Computational Biology > > Fred Hutchinson Cancer Research Center > > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > > > Location: M1-B861 > > Telephone: 206 667-2793 > > > > > > > -- > Computational Biology > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N. PO Box 19024 Seattle, WA 98109 > > Location: M1-B861 > Telephone: 206 667-2793 > [[alternative HTML version deleted]]