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 > >> > > >> > > > > > > [[alternative HTML version deleted]]