Search
Question: RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
0
gravatar for maeva.mollion
4 months ago by
maeva.mollion0 wrote:

Hello! 

I am currently trying to work with goslim on a set of differentially expressed genes of which I have some ontologies. 

I tried to use commands similar to those on this link https://www.rdocumentation.org/packages/GSEABase/versions/1.34.0/topics/goSlim-methods

fl <- system.file("extdata", "goslim_plant.obo", package="GSEABase")
slim <- getOBOCollection(fl)

setDEGOs=as.character(DEGOs$V3)
#head(setDEGOs)
#[1] "GO:0006354" "GO:0003677" "GO:0016570" "GO:0005515" "GO:0003702" "GO:0005815"
currentCollecSet=GOCollection(setDEGOs)

 

However, I obtain the following error when running GOCollection:

Error: getAnnMap: package GO not available

 

When I try to install the missing package, this is what I obtain:

>biocLite("GO")
BioC_mirror: https://bioconductor.org
Using Bioconductor 3.5 (BiocInstaller 1.26.1), R 3.4.1 (2017-06-30).
Installing package(s) ‘GO’
installation path not writeable, unable to update packages: boot, Matrix, mgcv
Warning message:
package ‘GO’ is not available (for R version 3.4.1) 

 

It seems my R installation is up to date. Any idea what is going on? Is there any other library I should use here? 

This is the result of my sessionInfo() command:

R version 3.4.1 (2017-06-30)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=Danish_Denmark.1252  LC_CTYPE=Danish_Denmark.1252    LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C                   
[5] LC_TIME=Danish_Denmark.1252    

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] GSEABase_1.38.1      graph_1.54.0         annotate_1.54.0      XML_3.98-1.9         AnnotationDbi_1.38.2 IRanges_2.10.3       S4Vectors_0.14.4    
 [8] Biobase_2.36.2       BiocGenerics_0.22.0  BiocInstaller_1.26.1

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.12   digest_0.6.12  bitops_1.0-6   xtable_1.8-2   DBI_0.7        RSQLite_2.0    rlang_0.1.2    blob_1.1.0     tools_3.4.1    bit64_0.9-7   
[11] RCurl_1.95-4.8 bit_1.1-12     compiler_3.4.1 memoise_1.1.0  tibble_1.3.4  

Best regards and thanks for reading!

ADD COMMENTlink modified 4 months ago • written 4 months ago by maeva.mollion0
1
gravatar for Martin Morgan
4 months ago by
Martin Morgan ♦♦ 21k
United States
Martin Morgan ♦♦ 21k wrote:

The missing package is GO.db, so biocLIte("GO.db").

ADD COMMENTlink written 4 months ago by Martin Morgan ♦♦ 21k

Thanks! It's working now that I've done that.

ADD REPLYlink written 4 months ago by maeva.mollion0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 155 users visited in the last hour