[BioC] Ensembl IDs 2 GO term enrichment --> simple solution without biomart? ( I can't install it because of RCurl)
Emmanuel Levy
emmanuel.levy at gmail.com
Fri Sep 19 20:18:56 CEST 2008
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_COLLATE=en_CA.UTF-8;LC_MONETARY=en_CA.UTF-8;LC_MESSAGES=en_CA.UTF-8;LC_PAPER=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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