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Old 02-18-2015, 12:52 AM   #1
rozitaa
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Default clusterProfiler a tool for GSE analysis

Hi,

currently I am using clusterProfiler for gene set analysis and pathway analysis. but it seems some of the functions in the manual cannot be found in the R! such as gseGO(), getGeneSet() or enrichMap() which might have been removed! Does anyone has any idea about this?

Or do you know any other package that does the same? plots gsea plots, visualizes enriched kegg pathways, or plots enriched gene set maps?

Thanks
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Old 03-12-2015, 07:17 PM   #2
ygc
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Please check the version of clusterProfiler installed in your system.

You definitely using an out-of-date version.


> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin14.1.0 (64-bit)

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] stats graphics grDevices utils datasets methods base

other attached packages:
[1] clusterProfiler_2.1.8 RSQLite_1.0.0 DBI_0.3.1
[4] magrittr_1.5

loaded via a namespace (and not attached):
[1] annotate_1.44.0 AnnotationDbi_1.29.17 AnnotationForge_1.8.2
[4] Biobase_2.27.1 BiocGenerics_0.13.4 Biostrings_2.35.11
[7] Category_2.32.0 colorspace_1.2-6 digest_0.6.8
[10] DO.db_2.8.0 DOSE_2.5.8 fortunes_1.5-2
[13] genefilter_1.48.1 GenomeInfoDb_1.3.13 ggplot2_1.0.0
[16] GO.db_3.0.0 GOSemSim_1.25.4 GOstats_2.32.0
[19] graph_1.45.1 grid_3.1.2 GSEABase_1.28.0
[22] gtable_0.1.2 httr_0.6.1 igraph_0.7.1
[25] IRanges_2.1.40 KEGG.db_3.0.0 KEGGREST_1.7.4
[28] lattice_0.20-30 MASS_7.3-39 Matrix_1.1-5
[31] munsell_0.4.2 parallel_3.1.2 plyr_1.8.1
[34] png_0.1-7 proto_0.3-10 qvalue_1.43.0
[37] RBGL_1.42.0 Rcpp_0.11.5 RDAVIDWebService_1.4.0
[40] reshape2_1.4.1 rJava_0.9-6 S4Vectors_0.5.21
[43] scales_0.2.4 splines_3.1.2 stats4_3.1.2
[46] stringr_0.6.2 survival_2.38-1 tools_3.1.2
[49] XML_3.98-1.1 xtable_1.7-4 XVector_0.7.4
[52] zlibbioc_1.13.1
>
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Old 03-16-2015, 07:07 AM   #3
rozitaa
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Quote:
Originally Posted by ygc View Post
Please check the version of clusterProfiler installed in your system.

You definitely using an out-of-date version.


> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin14.1.0 (64-bit)

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] stats graphics grDevices utils datasets methods base

other attached packages:
[1] clusterProfiler_2.1.8 RSQLite_1.0.0 DBI_0.3.1
[4] magrittr_1.5

loaded via a namespace (and not attached):
[1] annotate_1.44.0 AnnotationDbi_1.29.17 AnnotationForge_1.8.2
[4] Biobase_2.27.1 BiocGenerics_0.13.4 Biostrings_2.35.11
[7] Category_2.32.0 colorspace_1.2-6 digest_0.6.8
[10] DO.db_2.8.0 DOSE_2.5.8 fortunes_1.5-2
[13] genefilter_1.48.1 GenomeInfoDb_1.3.13 ggplot2_1.0.0
[16] GO.db_3.0.0 GOSemSim_1.25.4 GOstats_2.32.0
[19] graph_1.45.1 grid_3.1.2 GSEABase_1.28.0
[22] gtable_0.1.2 httr_0.6.1 igraph_0.7.1
[25] IRanges_2.1.40 KEGG.db_3.0.0 KEGGREST_1.7.4
[28] lattice_0.20-30 MASS_7.3-39 Matrix_1.1-5
[31] munsell_0.4.2 parallel_3.1.2 plyr_1.8.1
[34] png_0.1-7 proto_0.3-10 qvalue_1.43.0
[37] RBGL_1.42.0 Rcpp_0.11.5 RDAVIDWebService_1.4.0
[40] reshape2_1.4.1 rJava_0.9-6 S4Vectors_0.5.21
[43] scales_0.2.4 splines_3.1.2 stats4_3.1.2
[46] stringr_0.6.2 survival_2.38-1 tools_3.1.2
[49] XML_3.98-1.1 xtable_1.7-4 XVector_0.7.4
[52] zlibbioc_1.13.1
>
Thanks a lot! exactly that was the problem!
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