[BioC] Affy Tiling arrays & oligo

[James W. MacDonald]

Hi Joseph,

You might be able to analyze your data on a Windows box, but I don't 
think you will be able to create the platform design package, which is 
going to take lots of memory. Probably your best bet is to use a 64 bit 
Linux box with 6-8 Gb RAM.

Best,

Jim



joseph wrote:
> 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 at jhsph.edu>
> To: joseph <jdsandjd at yahoo.com>
> Cc: bioconductor at 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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-- 
James W. MacDonald, M.S.
Biostatistician
Affymetrix and cDNA Microarray Core
University of Michigan Cancer Center
1500 E. Medical Center Drive
7410 CCGC
Ann Arbor MI 48109
734-647-5623