[BioC] Cyclic Loess

[Martin Morgan]

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 at fhcrc.org
> <mailto:mtmorgan at 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]]
>     >
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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