[BioC] Cyclic Loess

[Martin Morgan]

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 = TRUE))
> 
> then to normlize i used
> 
> normalize.loess(exprs,epsilon=1,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
> 
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> 
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