[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
Thu Sep 18 03:23:52 CEST 2008
Dear Robert,
> That depends a bit on the organism you are wanting to use. For those that
> are supported by the org.xx.yy.db packages, such as human,
> org.Hs.eg
>
> there are maps in those annotation packages
> [9] "org.Hs.egENSEMBL2EG" "org.Hs.egENSEMBLPROT"
> [11] "org.Hs.egENSEMBLPROT2EG" "org.Hs.egENSEMBLTRANS"
> [13] "org.Hs.egENSEMBLTRANS2EG" "org.Hs.egENZYME"
>
Thank you for your reply, I indeed want to annotate human IDs, so the
org.Hs.eg.db package looks good!
However the help I could find on this package is limited. I understood
from the following page:
http://gaggle.systemsbiology.net/svn/gaggle/PIPE2.0/trunk/PIPEletResourceDir/GOTableEnrichment/GOEnrichmentScript.R
That "org.Hs.eg.db" can directly be given as the annotation package,
but then the IDs should be converted to EntrezIDs.
It took me some time to figure it out, but I guess that now I've got
to familiarize myself with:
http://www.cse.unsw.edu.au/~mike/myrlibrary/AnnotationDbi/html/Bimap.html
One question though, how to list the annotation packages as you did above?
> help.search("org.Hs.eg.db")
or
> org.Hs.eg.db()
didn't help.
Finally, I googled for the keywords "GOstats and biomart" and did not
find any page that shows how to use them together. (In fact my post
from yesterday appears in 3rd position!)
Is it so straightforward to use them together and I'm being slow? Or
are they incompatible?
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
>>
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>>
>
> --
> 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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