Hi and thank you for your answer Dr. Carvalho, I read the NDF manually. There are numbers from 1 to 461 in the PROBE_CLASS column. Is the solution to change the numbers into word "experimental"? Thank you, Zeynep 2012/4/24 Benilton Carvalho <beniltoncarvalho@gmail.com> > If you read the NDF manually, what are the values for the column > PROBE_CLASS? The builder expects to find the value "experimental"... And > yours does not seem to be the case. > > > On Tuesday, 24 April 2012, zeynep özkeserli wrote: > >> Hi all, >> >> I am trying to analyze Nimblegen Human 2.1 M Deluxe Promoter array data >> using Charm package. My problem is, when I try to import the xys data, >> program needs the platform design file, as usual, tries to download from >> BioConductor website but prompts out this error and stops. >> >> ... >> Loading required package: pd.100929.hg19.deluxe.prom.meth.hx1 >> Attempting to obtain 'pd.100929.hg19.deluxe.prom.meth.hx1' from >> BioConductor website. >> Checking to see if your internet connection works... >> Package 'pd.100929.hg19.deluxe.prom.meth.hx1' was not found in the >> BioConductor repository. >> The 'pdInfoBuilder' package can often be used in situations like this. >> ... >> >> >> So I tried the pdInfoBuilder package to solve my problem. But it also >> didn't work. Here is what I do and the errors I get: >> >> I took the code from this address and modified for myself: >> >> http://www.biostat.jhsph.edu/~maryee/charm/index.php/Main/MakingANe wArrayAnnotationPackage >> >> >> >> library(pdInfoBuilder) >> ndf <- list.files(pattern = ".ndf", full.names = TRUE) >> pos <- list.files(pattern = ".pos", full.names = TRUE) >> xys <- list.files(pattern = ".xys", full.names = TRUE)[1] >> seed <- new("NgsTilingPDInfoPkgSeed", >> ndfFile = ndf, xysFile = xys, >> posFile = pos, >> author = "Martin Aryee", >> version = "0.99.0", >> email = "myemail@jhu.edu", >> biocViews = "AnnotationData", >> genomebuild = "HG 18", organism = "Human", >> species = "Homo sapiens") >> makePdInfoPackage(seed, destDir = ".") >> >> >> *After the code worked for 2 hours, I got these errors:* >> >> >> >> Building annotation package for Nimblegen Tiling Array >> NDF: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf >> >> POS: 100929_HG19_Deluxe_Prom_Meth_HX1.pos >> XYS: 503534_532.xys >> >> =================================================================== =============== >> Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.ndf... OK >> Parsing file: 100929_HG19_Deluxe_Prom_Meth_HX1.pos... OK >> Merging NDF and POS files... OK >> Parsing file: 503534_532.xys... OK >> Creating package in ./pd.100929.hg19.deluxe.prom.meth.hx1 >> Inserting 30291 rows into table featureSet... OK >> Inserting 0 rows into table pmfeature... Error in >> sqliteExecStatement(con, statement, bind.data) : >> bind.data must have non-zero dimensions >> >> >> I really can't figure out what the problem is. Can anybody offer any >> solutions? >> >> Thank you in advance! :) >> >> Zeynep Ozkeserli >> Ankara University Biotechnology Institute >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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]]