[BioC] EBcoexpress error - initializeHP() error

[Dan Tenenbaum]

On Thu, Nov 29, 2012 at 3:08 PM, Seb <seba.bat at gmail.com> wrote:
> sure, the file is attached (it's 1.9mb 2796 rows per 58cols)
>
> the code that generated the error is:
>
> myHP <- initializeHP(D, cond)
>
> - D is the output matrix from
> D <- makeMyD (myData, cond)
>
> - cond is the conditions file, containing the header for the samples in the
> myData matrix
>


Thanks, but this still isn't complete. Can you send the code that
reads your data file into R, and also the code that creates 'myData'.
In other words, all the code starting from the beginning of the R
session to the error you get.

Thanks,
Dan


> thanks!!
>
> Seb
>
>
>
>
> On Thu, Nov 29, 2012 at 5:58 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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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>
>