[BioC] Problem importing ArrayExpress data for custom array into BioConductor

[Valerie Obenchain]

Hi Aatish,

It looks like the brainarray site does not have mac binaries available.
>From your browser visit,

    http://brainarray.mbni.med.umich.edu/bioc/bin/

Here you will see that brainarray currently has no macosx directory . 
One workaround for this is to use the source tarball.  Look in

    http://brainarray.mbni.med.umich.edu/bioc/src/contrib/

for the appropriate cdf package (ie, maybe one of
tilingscerevisiae10scense* ). Then from your R session try

    biocLite("tilingscerevisiae10rscensecdf",
contriburl="http://brainarray.mbni.med.umich.edu/bioc/src/contrib/",
type="source")


Alternatively you could download the tarball and build the package
manually. Having your own copy of the tarball might be a good idea if
you want guaranteed access to this cdf package for sometime.

Valerie


On 10/19/2010 11:15 PM, Aatish wrote:
> Hi, 
>
> I've been spending a lot of time trying to do something quite elementary and
> have been getting thoroughly stuck, so apologies in advance for the basic
> question.
>
> I've been trying to build an R object from CEL data from the ArrayExpress
> database. I used the ArrayExpress package for BioConductor to import the data. 
>
> Following the vignette, I ran:
>
> library("ArrayExpress")
> rawset = ArrayExpress("E-TABM-14")
>
> which downloaded all the data for this experiment. After downloading I get the
> message:
>
> Read 48 items
> The object containing experiment  E-TABM-14  has been built.
>
> However, if I try to access this data structure (which should be an AffyBatch
> file), I get the following error message:
>
> rawset 
>
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.11
> AffyBatch object
> size of arrays=2560x2560 features (32 kb)
> cdf=Scervisiae_tiling (??? affyids)
> number of samples=8
> Warning: unable to access index for repository
> http://brainarray.mbni.med.umich.edu/bioc/bin/macosx/leopard/contrib/2.11
> Error in getCdfInfo(object) : 
>   Could not obtain CDF environment, problems encountered:
> Specified environment does not contain Scervisiae_tiling
> Library - package scervisiaetilingcdf not installed
> Bioconductor - scervisiaetilingcdf not available
> In addition: Warning message:
> missing cdf environment! in show(AffyBatch) 
>
> As far as I know, there is no standard package called scervisiaetilingcdf. I
> assume that I am missing a CDF file that is for the customized Affymetrix S.
> Cerevisiae Tiling Microarray that was used to generate the data.  However, I
> don't know where I can obtain this CDF file from or how I can create it. I would
> be very appreciative if someone could point me in the right direction.
>
> Thanks for your help,
> Aatish Bhatia
> PhD. student, Rutgers University
>
> P.S. Here are the contents of:
>
> traceback()
> 7: stop(paste("Could not obtain CDF environment, problems encountered:",
> paste(unlist(badOut), collapse = "\n"), sep = "\n"))
> 6: getCdfInfo(object)
> 5: featureNames(object)
> 4: featureNames(object)
> 3: cat("number of genes=", length(featureNames(object)), "\n", sep = "")
> 2: function (object) 
>    standardGeneric("show")(<S4 object of class "AffyBatch">)
> 1: function (object) 
>    standardGeneric("show")(<S4 object of class "AffyBatch">)
>
> and
>
> sessionInfo()
> R version 2.11.1 (2010-05-31) 
> x86_64-apple-darwin9.8.0 
>
> locale:
> [1] en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base     
>
> other attached packages:
> [1] limma_3.4.5        affy_1.26.1        ArrayExpress_1.8.0 Biobase_2.8.0     
>
> loaded via a namespace (and not attached):
> [1] affyio_1.16.0         preprocessCore_1.10.0 tools_2.11.1         
> [4] XML_3.2-0
>
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