Hi all, I have run goseq on RNA-seq data differential expression results, but got a strange p-value distribution: from zero to almost one it is uniformly distributed, but there is a huge enrichment to the value one. See screenshot: https://dl.dropbox.com/u/18352887/Selection_042.png This seems that the distribution underlying the null hypothesis is incorrect? As a consequence, nearly all conditions I test do not have overrepresented GO categories. I do not trust the outcome of this. I've done goseq analysis with custom GO-mappings (from Biomart) and lengths file (from GenomicFeatures package) for the genome sacCer3 (gene database sgdGene). (when I tried the built-in genome, goseq failed to find the data automatically). Any help on how to interpret or to correct this? Thanks, Joachim Joachim Jacob, PhD Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 10/30/2012 08:53 AM, Dave Tang wrote: > Hello, > > I've been trying to install goseq on R-2.15.2 but one of the > dependencies, RCurl is not installing. I've compiled curl and > curl-config (7.28.0); there is also a system wide installation of curl > (7.15.5) in /usr/bin/. I tried installing just RCurl but to no avail. > I've looked online for help for hours but it has been hopeless. I > would be extremely grateful if someone could let me know what is wrong. > > source("http://bioconductor.org/biocLite.R") > biocLite("RCurl") > checking for curl-config... /home/davetang/bin/bin/curl-config > > [snipped] > > gcc -std=gnu99 -shared -L/usr/local/lib64 -o RCurl.so base64.o curl.o > curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o > -L/home/davetang/bin/curl/lib -lcurl -lxml2 -lz -lm > installing to /home/davetang/src/R-2.15.2/library/RCurl/libs > ** R > ** data > ** inst > ** preparing package for lazy loading > Creating a generic function for 'close' from package 'base' in package > 'RCurl' > ** help > *** installing help indices > ** building package indices > ** installing vignettes > ** testing if installed package can be loaded > Error in dyn.load(file, DLLpath = DLLpath, ...) : > unable to load shared object > '/home/davetang/src/R-2.15.2/library/RCurl/libs/RCurl.so': > libcurl.so.4: cannot open shared object file: No such file or directory > Error: loading failed > Execution halted > ERROR: loading failed > * removing '/home/davetang/src/R-2.15.2/library/RCurl' > > The downloaded source packages are in > '/tmp/Rtmp9heDvL/downloaded_packages' > Updating HTML index of packages in '.Library' > Making packages.html ... done > Warning message: > In install.packages(pkgs = pkgs, lib = lib, repos = repos, ...) : > installation of package 'RCurl' had non-zero exit status > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocInstaller_1.8.3 > > loaded via a namespace (and not attached): > [1] tools_2.15.2 > > Many thanks in adavance, >