[BioC] xps - creating ROOT scheme fi les

[Mark Cowley]

Hi Benilton,
i'm using oligo in a processing pipeline which runs out of RAM with >15 exon arrays, so I was considering switching to xps. However, i'm intrigued by your comment re 'if you think you have enough RAM for the expression matrix'. Are you implying that you can use oligo on quite large numbers of exon arrays & that it's only when you create the expression object that you'll run out of RAM?

cheers,
Mark
-----------------------------------------------------
Mark Cowley, PhD

Peter Wills Bioinformatics Centre
Garvan Institute of Medical Research, Sydney, Australia
-----------------------------------------------------

On 15/06/2010, at 9:11 PM, Benilton Carvalho wrote:

> Dear John,
> 
> Indeed, xps is one solution. If you're willing to try another
> approach, you can also use the oligo package. It's experimental, as
> described in one of the vignettes, but the following should get you
> going:
> 
> library(oligo)
> ## enable large dataset management
> library(ff)
> ## set a place for temp files
> ## otherwise it'll use the current dir
> ldPath("/path/to/temp")
> cels = list.celfiles()
> raw = read.celfiles(cels)
> core = rma(raw, target="core")
> exprsCore = exprs(core)
> ## save in a tab-delim file
> write.table.ffdf(as.ffdf(exprsCore), file="core.txt", sep="\t", quote=FALSE)
> ## if you think you have enough RAM for the expression matrix
> expression = exprsCore[]
> 
> In case you observe anything unexpected, let me know.
> 
> b
> 
> On 15 June 2010 11:43, John Coulthard <bahhab at hotmail.com> wrote:
>> 
>> Dear list
>> 
>> I've got 6x2 Human Exon 1.0 ST arrays to analyse and 3gB of ram so I believe I need to use xps.
>> The xps vignette, appendix A.1. says...
>> "we need to create ROOT scheme fi les directly from the A ymetrix source  files, which need to be downloaded
>>  first from the A ymetrix web site."
>> 
>> I think the web page I need to download from is...
>> http://www.affymetrix.com/browse/products.jsp?productId=131452&navMode=34000&navAction=jump&aId=productsNav#1_3
>> 
>> but there is no file that ends with ‘annot.csv’.  Should I rename one of the other annotation files? Which one?
>> 
>> The CDF file on this page says 'unsupported' so maybe I should be looking for CLF-, PGF-fi les, but they're not on this page either.
>> 
>> Can anyone help me out with what to download from where?
>> 
>> Thanks
>> John
>> 
>> 
>> 
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