RESOLVED- GSEAbase: problem with GOCollection (getAnnMap: package GO not availale)
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@maevamollion-13907
Last seen 5.2 years ago

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!

gene ontology gseabase • 1.3k views
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@martin-morgan-1513
Last seen 7 days ago
United States

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

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

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