[BioC] EBcoexpress error - initializeHP() error

[Dan Tenenbaum]

On Thu, Nov 29, 2012 at 3:25 PM, Seb <seba.bat at gmail.com> wrote:
> oh, of course, sorry!
>
> library(EBcoexpress)
>
> # read my data file into R (note: i used na.strings="n/a" cause a gene was
> named NA in an old dataset, but it's anyway NOT there anymore in the one
> imported)
> myData <- read.table("myFile.txt", header=T, row.names=1, na.strings="n/a")
>


OK, first of all you are reading in myFile.txt but the file you sent
is called Filter_MSKCC_PCa_mRNA.txt, hopefully we're talking about the
same file?



Also, na.strings means "missing values are represented in my file by
this string". The string "n/a" does not occur in your text file. Was
it "NA" or "n/a" that was in the file before?

> # create the conditions file
> cond <- c(rep(1, times=29), rep(2, times=29))
>
> # create first correlation matrix, this works fine
> D <- makeMyD (myData, cond)
>
> # try to use initializeHP function
> myHP <- initializeHP(D, cond)
> --> here is where i get the error after a few sec that it's running <--
>
> pls let me know if you need more info!...and thanks!


OK, I am getting the same error (on a Mac running BioC 2.11).
I don't know what's going on, I'm guessing something bogus in the input data.

Anyone else have a suggestion?

Dan


>
> Seb
>
>
> On Thu, Nov 29, 2012 at 6:17 PM, Dan Tenenbaum <dtenenba at fhcrc.org> wrote:
>>
>> 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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>> >> > Bioconductor at r-project.org
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>> >> > Search the archives:
>> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
>> >
>> >
>
>