Thanks for trying it out Dan!
Yes, i used myFile.txt in the mail as it was quicker to write

You are also correct that "n/a" does not occurred in my file. However, the
initial data file was bigger with more genes, one of them was called NA and
I couldn't read the file cause R warned me of an NA in the row.names... so
to have R accept it I used the na.strings parameter.

Thanks again and if anyone has any more suggestions it would be just great

Seb

-- sent from my DROID - -
On Nov 29, 2012 6:42 PM, "Dan Tenenbaum" <dtenenba@fhcrc.org> wrote:

> On Thu, Nov 29, 2012 at 3:25 PM, Seb <seba.bat@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@fhcrc.org>
> wrote:
> >>
> >> On Thu, Nov 29, 2012 at 3:08 PM, Seb <seba.bat@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@fhcrc.org>
> >> > wrote:
> >> >>
> >> >> Hi Sebastiano,
> >> >>
> >> >>
> >> >> On Thu, Nov 29, 2012 at 2:34 PM, Sebastiano [guest]
> >> >> <guest@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.
> >> >> >
> >> >> > _______________________________________________
> >> >> > Bioconductor mailing list
> >> >> > Bioconductor@r-project.org
> >> >> > https://stat.ethz.ch/mailman/listinfo/bioconductor
> >> >> > Search the archives:
> >> >> > http://news.gmane.org/gmane.science.biology.informatics.conductor
> >> >
> >> >
> >
> >
>

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