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

[Wolfgang Huber]

Hi Aatish

short answer: use the 'davidTiling' package.

long answer: the AffyBatch class is designed for Affymetrix probe-set 
oriented arrays (i.e. arrays with a certain number of probes per gene); 
E-TABM-14 uses a custom-designed tiling array, for which I am not aware 
of a CDF (one could be made, but I am not sure it would be useful).

One could argue that the 'ArrayExpress' package/function should not even 
allow you to load the E-TABM-14 dataset, from this specialised platform, 
if it is not able to produce a fully valid Bioconductor data object out 
of it; instead, it seems that it opts to provide you with a 
half-complete, somewhat useful data object, which you could use for some 
things, but which will break as soon as it tries to find its CDF 
annotation package (as happens to you).

Furthermore, see also:
http://www.ebi.ac.uk/huber-srv/David2006 and
http://steinmetzlab.embl.de/NFRsharing --> E-TABM-590

Hope this helps
	Wolfgang


Il Oct/20/10 8:15 AM, Aatish ha scritto:
> 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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