GOSemSim mgeneSim GO.BP calculation time
0
0
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 7 months ago
China/Guangzhou/Southern Medical Univer…
Hi, I've optimized the code for the next release. If you would like to have a try, please install GOSemSim (version >= 1.5.3) and re-run your script. You can use the following command to install the devel version of BioC: install.packages("GOSemSim", repos = " http://www.bioconductor.org/packages/devel/bioc") This devel version of GOSemSim will officially release in Oct 2 within BioC 2.11 release. Bests, Guangchuang Yu --~--~---------~--~----~------------~-------~--~----~ Department of Biochemistry & Molecular Biology College of Life Science and Technology Jinan University, 601 Huangpu Ave. W. Guangzhou 510632, P.R. China Tel: +86-20-85222677 Email: guangchuangyu@gmail.com guangchuangyu@jnu.edu.cn Publications: http://bit.ly/IpzxpH -~----------~----~----~----~------~----~------~--~--- On Wed, Aug 22, 2012 at 6:35 PM, Sandeep Amberkar [guest] < guest@bioconductor.org> wrote: > > Dear All, > > I am using GOSemSim package to calculate semantic similarity of genes > within a cluster, for all clusters derived from a clustering algorithm. I > use the mgeneSim function to carry out these calculations. The function > works fine for GO.MF and GO.CC ontologies but it seems to fail for GO.BP. > When given a list of Entrez identifiers, the function seems to be stuck for > a long time, thus requiring the R session to be terminated. No warning or > error messages are produced. I don't seem to understand this behaviour of > this function for GO.BP.. What could be wrong here? I would appreciate any > help in this regard. Thanks a lot in advance. > > Please find attached sample Entrez IDs used for the calculation and my R > session info. > > -- output of sessionInfo(): > > Entrez ids = > 1132,1147,1326,1540,1654,1831,1917,2058,2289,3301,3305,3310,3312,331 3,3320,3326,3376,3476,3551,4790,4791,4792,4793,4794,5151,5495,5537,564 6,5917,5966,5970,5971,5977,6885,7098,7128,7132,7185,7278,7763,8517,851 8,8717,8737,8767,8915,9020,9253,9532,9701,9755,10010,10293,10318,10382 ,10454,10758,10848,10892,11035,11140,22870,23085,23118,23243,23291,234 74,26133,26610,28511,28512,29110,29775,54765,55140,55250,55291,55728,5 7805,64170,64332,64343,79092,79155,81030,84433,89891,92609,113457,1363 19,148022,150684,203068,257397,347733,387521,387522 > > OS -- opensuse 12.1 > > sessionInfo() > R version 2.15.1 (2012-06-22) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_GB.UTF-8 LC_NUMERIC=C > LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8 > [5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8 LC_PAPER=C > LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] org.Hs.eg.db_2.7.1 igraph_0.6-2 GOSemSim_1.14.0 > BiocInstaller_1.4.7 AnnotationDbi_1.18.1 > [6] Biobase_2.16.0 BiocGenerics_0.2.0 RSQLite_0.11.1 > DBI_0.2-5 > > loaded via a namespace (and not attached): > [1] GO.db_2.7.1 IRanges_1.14.4 stats4_2.15.1 tools_2.15.1 > > -- > Sent via the guest posting facility at bioconductor.org. > [[alternative HTML version deleted]]
GO GOSemSim GO GOSemSim • 739 views
ADD COMMENT

Login before adding your answer.

Traffic: 244 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