[BioC] EBcoexpress error - initializeHP() error

[Dan Tenenbaum]

Hi Sebastiano,


On Thu, Nov 29, 2012 at 2:34 PM, Sebastiano [guest]
<guest at bioconductor.org> wrote:
>
> hi all
>
> i'm using the EBcoexpress package to analyze a series of 29 Tumor vs 29 Normal cancer microarray data.
>
> following the directions in the pdf file i can create the first coexpression matrix with no errors, however, when i run the initializeHP() function (as decscribed in the package file) i get the following error:
>
> Error in mvnX(data = data, prior = prior):
> NA/NaN/Inf in foreign function call (arg 1)
>
> i removed all the zeroes (i had 8) in the input matrix but still i get the same error.
>

Can you attach or post your input data and send the code that produced
the errror?

>  -- output of sessionInfo():
>
> R version 2.15.1 (2012-06-22)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C
> [5] LC_TIME=English_United States.1252
>
> attached base packages:
> [1] splines   stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
>  [1] DCGL_1.02           igraph_0.6-3        Hmisc_3.10-1        survival_2.36-14    EBcoexpress_1.0.0   minqa_1.2.1         Rcpp_0.10.1         mclust_4.0          EBarrays_2.20.0
> [10] lattice_0.20-10     Biobase_2.16.0      BiocGenerics_0.2.0  BiocInstaller_1.4.9
>

Looks like you are still running BioC 2.10. You might want to upgrade
to BioC 2.11 as described here:

http://bioconductor.org/install/#bioc-version

Dan


> loaded via a namespace (and not attached):
> [1] cluster_1.14.3 grid_2.15.1    tools_2.15.1
>
> --
> Sent via the guest posting facility at bioconductor.org.
>
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