Question: Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to create gene sets: invalid BroadCollection category: 'archived'
0
gravatar for rached
21 months ago by
rached40
rached40 wrote:

I receive an error when I attempt to load the latest version of the MSigDB xml file (version 6.1):

> MSigDB <- getBroadSets('msigdb_v6.1.xml');
Error: 'getBroadSets' failed to create gene sets:
  invalid BroadCollection category: 'archived'

Is anyone aware of a possible solution?

> sessionInfo();
R version 3.3.2 (2016-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)
Running under: macOS  10.13.1

locale:
[1] en_CA.UTF-8/en_CA.UTF-8/en_CA.UTF-8/C/en_CA.UTF-8/en_CA.UTF-8

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

other attached packages:
[1] GSEABase_1.36.0      graph_1.52.0         annotate_1.52.1      XML_3.98-1.9         AnnotationDbi_1.36.2 IRanges_2.8.2        S4Vectors_0.12.2
[8] Biobase_2.34.0       BiocGenerics_0.20.0

loaded via a namespace (and not attached):
[1] Rcpp_0.12.14   digest_0.6.13  bitops_1.0-6   xtable_1.8-2   DBI_0.7        RSQLite_2.0    rlang_0.1.4    blob_1.1.0     tools_3.3.2    bit64_0.9-7
[11] RCurl_1.95-4.8 bit_1.1-12     memoise_1.1.0  tibble_1.3.4
ADD COMMENTlink modified 21 months ago by Robert Castelo2.3k • written 21 months ago by rached40
Answer: Error thrown by GSEABase::getBroadSets function: Error: 'getBroadSets' failed to
2
gravatar for Robert Castelo
21 months ago by
Robert Castelo2.3k
Spain/Barcelona/Universitat Pompeu Fabra
Robert Castelo2.3k wrote:

hi,

I've just tried it out with the current release version of R 3.4.2 and the GSEABase package (1.40.1) and it works fine. You need to update to the  current R release version 3.4.2 and current release of Bioconductor; see http://bioconductor.org/install.

library(GSEABase)
MSigDB <- getBroadSets('msigdb_v6.1.xml')
MSigDB
GeneSetCollection
  names: AAANWWTGC_UNKNOWN, AAAYRNCTG_UNKNOWN, ..., GRYDER_PAX3FOXO1_ENHANCERS_KO_DOWN (18650 total)
  unique identifiers: MEF2C, ATP1B1, ..., Ano3 (32445 total)
  types in collection:
    geneIdType: SymbolIdentifier (1 total)
    collectionType: BroadCollection (1 total)

Here my session info:

sessionInfo()
R version 3.4.2 (2017-09-28)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Sierra 10.12.6

Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] GSEABase_1.40.1      graph_1.56.0         annotate_1.56.1     
 [4] XML_3.98-1.9         AnnotationDbi_1.40.0 IRanges_2.12.0      
 [7] S4Vectors_0.16.0     Biobase_2.38.0       BiocGenerics_0.24.0
[10] colorout_1.1-2      

loaded via a namespace (and not attached):
 [1] Rcpp_0.12.14   digest_0.6.12  bitops_1.0-6   xtable_1.8-2   DBI_0.7       
 [6] RSQLite_2.0    rlang_0.1.4    blob_1.1.0     bit64_0.9-7    RCurl_1.95-4.8
[11] bit_1.1-12     compiler_3.4.2 memoise_1.1.0  tibble_1.3.4  

 

ADD COMMENTlink modified 21 months ago • written 21 months ago by Robert Castelo2.3k

getBroadSets successfully ran after I updated R and GSEABase to match the versions you mentioned.

Thank you!

ADD REPLYlink written 21 months ago by rached40
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