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>
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> >     > Search the archives:
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> >
> >
> >     --
> >     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
>

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