Hi Benilton
I am using 
    the Mouse Promoter 1.0R Array.
So far I have not been sucessuful to create the platform design environment.  Please see the error and the sessionInfo() below. Also, can you please point out to me Naira's document you mentioned, or you are referring to her last month entry "Oligo package and tiling arrays - PM and MM" .
Joseph




>
makePDpackage("Mm_PromPR_v01_NCBIv35.bpmap",manufacturer="affymetrix",
type="tiling")


affymetrix tiling 


The package will be called pd.mm.prompr.v01.ncbiv35 


Error: cannot allocate vector of size 16.1 Mb


In addition: Warning messages:


1: In names(tmp)[10] <- "chromosome" :


  Reached total
allocation of 1535Mb: see help(memory.size)


2: In names(tmp)[10] <- "chromosome" :


  Reached total
allocation of 1535Mb: see help(memory.size)


3: In names(tmp)[10] <- "chromosome" :


  Reached total
allocation of 1535Mb: see help(memory.size)


4: In names(tmp)[10] <- "chromosome" :


  Reached total
allocation of 1535Mb: see help(memory.size)


> sessionInfo()


R version 2.6.1 Patched (2007-12-08 r43617) 


i386-pc-mingw32 


locale:


LC_COLLATE=English_United
States.1252;LC_CTYPE=English_United States.1252;LC_MONETARY=English_United
States.1252;LC_NUMERIC=C;LC_TIME=English_United States.1252


attached base packages:


[1] splines  
tools     stats     graphics 
grDevices utils     datasets  methods  
base     


other attached packages:


 [1]
makePlatformDesign_1.2.0 oligo_1.2.2              oligoClasses_1.0.3       affxparser_1.10.2       


 [5] AnnotationDbi_1.0.6      preprocessCore_1.0.0     RSQLite_0.6-4            DBI_0.2-4               


 [9] Biobase_1.16.1           affyio_1.6.1
----- Original Message ----
From: Benilton Carvalho <bcarvalh@jhsph.edu>
To: joseph <jdsandjd@yahoo.com>
Cc: bioconductor@stat.math.ethz.ch
Sent: Wednesday, December 12, 2007 8:31:38 AM
Subject: Re: Affy Tiling arrays & oligo


Dear Joseph,

As of now, oligo can read in the intensities for your CEL files, if you create the platform design environment as described by Naira. I don't have specific methods implemented yet in oligo for tiling arrays, but you can benefit if other packages do and use standard Biobase objects.


What array are you using?


b

On Dec 12, 2007, at 11:25 AM, joseph wrote:

Hello
The vignette "An Introduction to the Oligo Package" addresses only Affymetrix SNP Arrays. Does any one have an example of how to analyze Affy tiling arrays with oligo and is willing to share it?
Thanks
Joseph Dhahbi
CHORI













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