Question: Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
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gravatar for Emmanuel Levy
11.1 years ago by
Emmanuel Levy270
Emmanuel Levy270 wrote:
Thanks for your quick reply - so my first guess was correct: there is no obvious compatibility between GOstats and biomaRt. I'll use NCBI's data then! Best wishes, Emmanuel 2008/9/19 Robert Gentleman <rgentlem at="" fhcrc.org="">: > Hi, > Best to keep discussions on the list. The answer to that is I don't know > what you would need to do, and don't have use cases for this, so I won't be > able to help > > > Emmanuel Levy wrote: >> >> Dear Robert, >> >>> gU = mappedLkeys(org.Hs.egENSEMBL) >>> selIds = sample(gU, 100) >>> >>> replace the two lines above with your data - gU is the universe >>> (translate >>> to EG by using org.Hs.eg.db) and selIds are the interesting IDs. >>> >>> params = new("GOHyperGParams", geneIds = selIds, >>> universeGeneIds = gU, annotation="org.Hs.eg.db", >>> ontology="BP", pvalueCutoff = 0.01, conditional=FALSE, >>> testDirection = "over") >> >> Thanks for your answer - I actually figured out how to use GOstats >> with "org.Hs.eg.db", but what I did not understand was how to use it >> with biomart. As far as I'm aware of, GO annotations can be retrieved >> with the getGO function, but biomart does not (maybe I'm wrong?) >> provide an environment that maps protein IDs to GO terms. This is why >> I'm wondering which annotation package I should give to GOStats in >> order to use biomart but not "org.Hs.eg.db". >> >> I apologize for bothering you with still the same question. >> >> Best wishes, >> >> Emmanuel >> >> >>> hgO = hyperGTest(params) >>> >>> should do it. >>> >>>> hg0 >>> >>> Error: object "hg0" not found >>>> >>>> hgO >>> >>> Gene to GO BP test for over-representation >>> 494 GO BP ids tested (15 have p < 0.01) >>> Selected gene set size: 65 >>> Gene universe size: 13129 >>> Annotation package: org.Hs.eg.db >>>> >>>> Many thanks, >>>> >>>> Emmanuel >>>> >>>> >>>> >>>>>> Any hint would be greatly appreciated! >>>>>> >>>>>> Many thanks, >>>>>> >>>>>> Emmanuel >>>>>> >>>>>> >>>>>> >>>>>>> best wishes >>>>>>> Robert >>>>>>> >>>>>>>> Thanks again for your help! >>>>>>>> >>>>>>>> Best wishes, >>>>>>>> >>>>>>>> Emmanuel >>>>>>>> >>>>>>>> >>>>>>>>>> Though I have problems installing biomaRt, which I reported to the >>>>>>>>>> R >>>>>>>>>> mailing list, I was wondering how to use GOstats with biomaRt, >>>>>>>>>> i.e., >>>>>>>>>> what should be specified for the "annotation package"? >>>>>>>>> >>>>>>>>> I think that that discussion suggested an upgrade of R (which you >>>>>>>>> will >>>>>>>>> need >>>>>>>>> for the tools I have described as well). >>>>>>>>> >>>>>>>>> best wishes >>>>>>>>> Robert >>>>>>>>> >>>>>>>>>> Also, I was wondering if by any chance, somebody could think of a >>>>>>>>>> way >>>>>>>>>> around biomaRt if I can't manage to install it. >>>>>>>>>> >>>>>>>>>> Many thanks for your help, >>>>>>>>>> >>>>>>>>>> Best wishes, >>>>>>>>>> >>>>>>>>>> Emmanuel >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> ========================================== >>>>>>>>>> Email sent to the R mailing list: >>>>>>>>>> >>>>>>>>>> Subject: RCurl compilation error on ubuntu hardy >>>>>>>>>> >>>>>>>>>> Dear list members, >>>>>>>>>> >>>>>>>>>> I encountered this problem and the solution pointed out in a >>>>>>>>>> previous >>>>>>>>>> thread did not work for me. >>>>>>>>>> (e.g. install.packages("RCurl", repos = >>>>>>>>>> "http://www.omegahat.org/R") >>>>>>>>>> >>>>>>>>>> I work with Ubuntu Hardy, and installed R 2.6.2 via apt- get. >>>>>>>>>> >>>>>>>>>> I really need RCurl in order to use biomaRt ... any help would be >>>>>>>>>> greatly appreciated. >>>>>>>>>> >>>>>>>>>> Best wishes, >>>>>>>>>> >>>>>>>>>> Emmanuel >>>>>>>>>> >>>>>>>>>> ================================================= >>>>>>>>>> >>>>>>>>>>> sessionInfo() >>>>>>>>>> >>>>>>>>>> R version 2.6.2 (2008-02-08) >>>>>>>>>> x86_64-pc-linux-gnu >>>>>>>>>> >>>>>>>>>> locale: >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> LC_CTYPE=en_CA.UTF-8;LC_NUMERIC=C;LC_TIME=en_CA.UTF-8;LC_CO LLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_P APER=en_CA.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT= en_CA.UTF-8;LC_IDENTIFICATION=C >>>>>>>>>> >>>>>>>>>> attached base packages: >>>>>>>>>> [1] stats graphics grDevices utils datasets methods >>>>>>>>>> base >>>>>>>>>> >>>>>>>>>> loaded via a namespace (and not attached): >>>>>>>>>> [1] rcompgen_0.1-17 tools_2.6.2 >>>>>>>>>> >>>>>>>>>> ================================================= >>>>>>>>>> >>>>>>>>>> >>>>>>>>>>> install.packages("RCurl", repos = "http://www.omegahat.org/R") >>>>>>>>>> >>>>>>>>>> Warning in install.packages("RCurl", repos = >>>>>>>>>> "http://www.omegahat.org/R") >>>>>>>>>> : >>>>>>>>>> argument 'lib' is missing: using '/usr/local/lib/R/site- library' >>>>>>>>>> trying URL >>>>>>>>>> 'http://www.omegahat.org/R/src/contrib/RCurl_0.9-4.tar.gz' >>>>>>>>>> Content type 'application/x-gzip' length 150884 bytes (147 Kb) >>>>>>>>>> opened URL >>>>>>>>>> ================================================== >>>>>>>>>> downloaded 147 Kb >>>>>>>>>> >>>>>>>>>> * Installing *source* package 'RCurl' ... >>>>>>>>>> checking for curl-config... /usr/bin/curl-config >>>>>>>>>> checking for gcc... gcc >>>>>>>>>> checking for C compiler default output file name... a.out >>>>>>>>>> checking whether the C compiler works... yes >>>>>>>>>> checking whether we are cross compiling... no >>>>>>>>>> checking for suffix of executables... >>>>>>>>>> checking for suffix of object files... o >>>>>>>>>> checking whether we are using the GNU C compiler... yes >>>>>>>>>> checking whether gcc accepts -g... yes >>>>>>>>>> checking for gcc option to accept ANSI C... none needed >>>>>>>>>> checking how to run the C preprocessor... gcc -E >>>>>>>>>> Version has a libidn field >>>>>>>>>> configure: creating ./config.status >>>>>>>>>> config.status: creating src/Makevars >>>>>>>>>> ** libs >>>>>>>>>> gcc -std=gnu99 -I/usr/share/R/include -I/usr/share/R/include >>>>>>>>>> -DHAVE_LIBIDN_FIELD=1 -fpic -g -O2 -c base64.c -o base64.o >>>>>>>>>> In file included from base64.c:1: >>>>>>>>>> Rcurl.h:52: error: expected specifier-qualifier-list before >>>>>>>>>> 'cetype_t' >>>>>>>>>> make: *** [base64.o] Error 1 >>>>>>>>>> chmod: cannot access `/usr/local/lib/R/site- library/RCurl/libs/*': >>>>>>>>>> No >>>>>>>>>> such file or directory >>>>>>>>>> ERROR: compilation failed for package 'RCurl' >>>>>>>>>> ** Removing '/usr/local/lib/R/site-library/RCurl' >>>>>>>>>> >>>>>>>>>> The downloaded packages are in >>>>>>>>>> /tmp/RtmpQ8FMBZ/downloaded_packages >>>>>>>>>> Warning message: >>>>>>>>>> In install.packages("RCurl", repos = "http://www.omegahat.org/R") >>>>>>>>>> : >>>>>>>>>> installation of package 'RCurl' had non-zero exit status >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> =========================================================== ===================== >>>>>>>>>> >>>>>>>>>> Hi Martin, >>>>>>>>>> are you working on a 64-bit linux distribution and which version >>>>>>>>>> of >>>>>>>>>> RCurl are you trying to install? There has been a problem with a >>>>>>>>>> recent version of RCurl and the "R_base64_decode", search the >>>>>>>>>> archives >>>>>>>>>> of the Bioconductor mailing list for a thread called >>>>>>>>>> "RCurl loading problem with 64 bit linux distribution". >>>>>>>>>> Please try using the newest versions of R (R-2.7.0 has been >>>>>>>>>> released >>>>>>>>>> a >>>>>>>>>> few weeks ago) and RCurl, which you can obtain from within R by >>>>>>>>>> typing: >>>>>>>>>> install.packages("RCurl", repos = "http://www.omegahat.org/R") >>>>>>>>>> The new version of RCurl (>= 0.9.2) worked fine for me, while >>>>>>>>>> 0.9.0 >>>>>>>>>> and 0.9.1 did not. >>>>>>>>>> Hope this helps. >>>>>>>>>> Joern >>>>>>>>>> >>>>>>>>>> >>>>>>>>>> martin sikora wrote: >>>>>>>>>> >>>>>>>>>> dear list members, >>>>>>>>>> >>>>>>>>>> i'm having a problem installing the biomaRt package on my linux >>>>>>>>>> machine, due to the fact of a compilation error with RCurl. i am >>>>>>>>>> using >>>>>>>>>> R 2.6.2 on fedora 7, and this is the output i get: >>>>>>>>>> >>>>>>>>>> gcc -m32 -std=gnu99 -I/usr/include/R -I/usr/include/R >>>>>>>>>> -DHAVE_LIBIDN_FIELD=1 -I/usr/local/include -fpic -O2 -g -pipe >>>>>>>>>> -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack- protector >>>>>>>>>> --param=ssp-buffer-size=4 -m32 -march=i386 -mtune=generic >>>>>>>>>> -fasynchronous-unwind-tables -c base64.c -o base64.o >>>>>>>>>> In file included from base64.c:1: >>>>>>>>>> Rcurl.h:52: error: expected specifier-qualifier-list before >>>>>>>>>> ?cetype_t? >>>>>>>>>> base64.c: In function ?R_base64_decode?: >>>>>>>>>> base64.c:25: warning: pointer targets in assignment differ in >>>>>>>>>> signedness >>>>>>>>>> base64.c:39: warning: pointer targets in passing argument 1 of >>>>>>>>>> ?Rf_mkString? differ in signedness >>>>>>>>>> base64.c: In function ?R_base64_encode?: >>>>>>>>>> base64.c:60: warning: pointer targets in assignment differ in >>>>>>>>>> signedness >>>>>>>>>> make: *** [base64.o] Error 1 >>>>>>>>>> >>>>>>>>>> as far as i know i have all the necessary libraries installed: >>>>>>>>>> >>>>>>>>>> $ yum list installed | grep libxml >>>>>>>>>> libxml2.i386 2.6.31-1.fc7 >>>>>>>>>> installed libxml2-devel.i386 >>>>>>>>>> 2.6.31-1.fc7 >>>>>>>>>> installed libxml2-python.i386 >>>>>>>>>> 2.6.31-1.fc7 installed perl-libxml- perl.noarch >>>>>>>>>> 0.08-1.2.1 installed >>>>>>>>>> $ yum list installed | grep curl >>>>>>>>>> curl.i386 7.16.4-1.fc7 >>>>>>>>>> installed curl-devel.i386 >>>>>>>>>> 7.16.4-1.fc7 >>>>>>>>>> installed python-pycurl.i386 >>>>>>>>>> 7.16.0-0.1.20061207.fc installed >>>>>>>>>> >>>>>>>>>> as i am not an expert in linux stuff, i was wondering if there >>>>>>>>>> could be any other missing libraries? any other ideas? >>>>>>>>>> >>>>>>>>>> cheers >>>>>>>>>> martin >>>>>>>>>> >>>>>>>>>> _______________________________________________ >>>>>>>>>> Bioconductor mailing list >>>>>>>>>> Bioconductor at stat.math.ethz.ch >>>>>>>>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>>>>>>>> Search the archives: >>>>>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>>>>>>>> >>>>>>>>> -- >>>>>>>>> Robert Gentleman, PhD >>>>>>>>> Program in Computational Biology >>>>>>>>> Division of Public Health Sciences >>>>>>>>> Fred Hutchinson Cancer Research Center >>>>>>>>> 1100 Fairview Ave. N, M2-B876 >>>>>>>>> PO Box 19024 >>>>>>>>> Seattle, Washington 98109-1024 >>>>>>>>> 206-667-7700 >>>>>>>>> rgentlem at fhcrc.org >>>>>>>>> >>>>>>> -- >>>>>>> Robert Gentleman, PhD >>>>>>> Program in Computational Biology >>>>>>> Division of Public Health Sciences >>>>>>> Fred Hutchinson Cancer Research Center >>>>>>> 1100 Fairview Ave. N, M2-B876 >>>>>>> PO Box 19024 >>>>>>> Seattle, Washington 98109-1024 >>>>>>> 206-667-7700 >>>>>>> rgentlem at fhcrc.org >>>>>>> >>>>> -- >>>>> Robert Gentleman, PhD >>>>> Program in Computational Biology >>>>> Division of Public Health Sciences >>>>> Fred Hutchinson Cancer Research Center >>>>> 1100 Fairview Ave. N, M2-B876 >>>>> PO Box 19024 >>>>> Seattle, Washington 98109-1024 >>>>> 206-667-7700 >>>>> rgentlem at fhcrc.org >>>>> >>> -- >>> Robert Gentleman, PhD >>> Program in Computational Biology >>> Division of Public Health Sciences >>> Fred Hutchinson Cancer Research Center >>> 1100 Fairview Ave. N, M2-B876 >>> PO Box 19024 >>> Seattle, Washington 98109-1024 >>> 206-667-7700 >>> rgentlem at fhcrc.org >>> > > -- > Robert Gentleman, PhD > Program in Computational Biology > Division of Public Health Sciences > Fred Hutchinson Cancer Research Center > 1100 Fairview Ave. N, M2-B876 > PO Box 19024 > Seattle, Washington 98109-1024 > 206-667-7700 > rgentlem at fhcrc.org >
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