[BioC] Processing exon array in bioconductor

cstrato cstrato at aon.at
Fri Dec 19 00:17:46 CET 2008

Dear Jim

Thank you for mentioning xps as one of the available options for exon 

Regarding the memory needed, xps needs machines with 1 GB RAM only.
I have tested this with HuExon arrays for Windows XP, Mac OS X and Linux.

C.h.r.i.s.t.i.a.n   S.t.r.a.t.o.w.a
V.i.e.n.n.a           A.u.s.t.r.i.a
e.m.a.i.l:        cstrato at aon.at

James W. MacDonald wrote:
> Hi Jennifer,
> Barb, Jennifer (NIH/CIT) [E] wrote:
>> Hello All, I am fairly new to processing exon array CEL files using
>> the Affy package in Bioconductor and I was trying to obtain RMA
>> values for 6 chips on the Human Exon 1.0 st array and I received the
>> following error message after the rma command was run:
>>> eset<-rma(data)
> The affy package is not designed to work with the exon arrays. There 
> are three packages designed to analyze these arrays; oligo, xps, and 
> exonmap. I just wrote a blurb that will (or maybe has) appear on the 
> BioC website, showing what is required for such things. The relevant 
> portion looks like this:
> Affymetrix Exon ST Arrays:
>  oligo
>  - Requires a pdInfoPackage built using pdInfoBuilder
>  - This package collates cdf, probe, annotation data together
>  - These packages are available from Bioconductor via biocLite()
>  exonmap
>  - Requires installation of MySQL and Ensembl core database tables
>  - Requires specially modified cdf (available at
>    http://xmap.picr.man.ac.uk/download/) and affy package
>  xps
>  - Requires installation of ROOT
>  - Uses data files from Affymetrix (.CDF, .PGF, .CLF, .CSV) directly
> The part about the pdInfoPackage being available appears not to be 
> quite true as yet. We built them, but there were a couple of technical 
> aspects that need to get fixed before they will be downloadable via 
> biocLite(). And I have no idea how long that might take, although if 
> Marc Carlson sees this he may chime in.
> In the interim you could build your own using pdInfoBuilder. However, 
> for the exon arrays you will need a 64-bit linux box with something 
> like 8 Gb RAM to use either oligo or exonmap, due to the amount of 
> memory these things require. You might be able to use xps on Windows 
> with say 4 Gb RAM, but I am not sure about that.
> Another R solution is aroma.affymetrix which has its own mailing list 
> - you can google to find more information about that.
> Best,
> Jim
>> Error in getCdfInfo(object) : Could not obtain CDF environment,
>> problems encountered: Specified environment does not contain
>> HuEx-1_0-st-v2 Library - package huex10stv2cdf not installed 
>> Bioconductor - could not connect In addition: Warning message: In
>> readLines(biocURL) : cannot open: HTTP status was '503 Service
>> Unavailable'
>> I am under the impression that exon arrays have different library
>> files than the traditional cdf files used for the IVT expression
>> arrays.  The 4 library files for the exon array exist with the
>> following extensions:  .mps, .clf, .pgf, .qcc.  Is there something
>> special needed for processing exon arrays in bioconductor? Thank you,
>>  Jennifer
>> [[alternative HTML version deleted]]
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