Nimblegen promoter medip array platform design file problem
0
0
Entering edit mode
@zeynep-ozkeserli-5250
Last seen 9.9 years ago
Turkey
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]]
BiocViews Annotation Organism biocViews pdInfoBuilder charm BiocViews BiocViews Annotation • 1.4k views
ADD COMMENT

Login before adding your answer.

Traffic: 474 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6