[BioC] Using FLUSH filter in Human Gene ST Arrays

[Martin Morgan]

On 12/15/2010 07:35 AM, Oriol SENAN wrote:
> Dear List
> 
> I wonder if any of you may have used package "FLUSH.LVS.bundle" with
> Affymetrix Gene 1.0 ST arrays. I get an error when processing the RA object.
> I supose this error is related because initially was designed to use with
> arrays with mm probes, but in principle you can use without it, for the
> moment I cannot handle to solve it, but I think the solution may be
> possible. Here is the code and the error I get.
> 
> Thank you very much.
> 
> library("affy")
> library("FLUSH.LVS.bundle")

Hi Oriol -- FLUSH.LVS.bundle is not a Bioconductor package; you're
likely to get better help by communicating with the package maintainer
directly.

  packageDescription('FLUSH.LVS.bundle')$Maintainer

Martin

> data <- ReadAffy()
> RA.fit <- compute.RA(data)
> 
> Fitting models
> |                    |
> |#Error in t(contr.helmert(nprobes)) :
>   error in evaluating the argument 'x' in selecting a method for function
> 't'
> 
> traceback()
> 6: t(contr.helmert(nprobes))
> 5: as.vector(data)
> 4: matrix(rep(t(contr.helmert(nprobes)), nsamples), byrow = T, ncol =
> nprobes -
>        1)
> 3: make.design(nsamples = nsamples, nprobes = tabProbes[i])
> 2: compute.RA(data)
> 1: compute.RA(data)
> 
> sessionInfo()
> 
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
> 
> locale:
>  [1] LC_CTYPE=ca_ES.utf8       LC_NUMERIC=C
>  [3] LC_TIME=ca_ES.utf8        LC_COLLATE=ca_ES.utf8
>  [5] LC_MONETARY=C             LC_MESSAGES=ca_ES.utf8
>  [7] LC_PAPER=ca_ES.utf8       LC_NAME=C
>  [9] LC_ADDRESS=C              LC_TELEPHONE=C
> [11] LC_MEASUREMENT=ca_ES.utf8 LC_IDENTIFICATION=C
> 
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
> 
> other attached packages:
> [1] hugene10stv1cdf_2.7.1  FLUSH.LVS.bundle_1.3.1 affyPLM_1.26.0
> [4] preprocessCore_1.12.0  gcrma_2.22.0           quantreg_4.53
> [7] SparseM_0.86           affy_1.28.0            Biobase_2.10.0
> 
> loaded via a namespace (and not attached):
> [1] affyio_1.18.0        AnnotationDbi_1.12.0 Biostrings_2.18.2
> [4] DBI_0.2-5            IRanges_1.8.4        RSQLite_0.9-4
> [7] splines_2.12.0       tools_2.12.0
> 
> Oriol Senan Campos
> Non Linear Dynamics Non Linear Optics Group
> Universitat Politècnica de Catalunya, Campus de Terrasa
> * +34 93 739 *8835
> 
> 	[[alternative HTML version deleted]]
> 
> 
> 
> 
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