Entering edit mode
3.2 years ago
ansonkn
•
0
Running clusterprofiler GSEA in R wit the following command.
GSEA(geneList = gl, TERM2GENE = sig, pvalueCutoff = 1) where sig s a data frame containing three different gene sets and associated genes (75 each) in two columns and gl is a vector of logFC with gene symbol.
GSEA however only return gene sets that are significant regardless of pvaluecutoff values. Any ideas?
R version 4.0.3 (2020-10-10)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Catalina 10.15.7
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/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] parallel stats4 grid stats graphics
[6] grDevices utils datasets methods base
other attached packages:
[1] tidyr_1.1.2
[2] wesanderson_0.3.6
[3] edgeR_3.32.1
[4] variancePartition_1.20.0
[5] scales_1.1.1
[6] BiocParallel_1.24.1
[7] limma_3.46.0
[8] GSVA_1.38.1
[9] org.Hs.eg.db_3.12.0
[10] AnnotationDbi_1.52.0
[11] msigdbr_7.2.1
[12] stringr_1.4.0
[13] clusterProfiler_3.18.0
[14] EnhancedVolcano_1.8.0
[15] ggrepel_0.9.1
[16] DESeq2_1.30.0
[17] SummarizedExperiment_1.20.0
[18] Biobase_2.50.0
[19] MatrixGenerics_1.2.1
[20] matrixStats_0.58.0
[21] GenomicRanges_1.42.0
[22] GenomeInfoDb_1.26.2
[23] IRanges_2.24.1
[24] S4Vectors_0.28.1
[25] BiocGenerics_0.36.0
[26] VennDiagram_1.6.20
[27] futile.logger_1.4.3
[28] pheatmap_1.0.12
[29] RColorBrewer_1.1-2
[30] dplyr_1.0.4
[31] tibble_3.0.6
[32] gridExtra_2.3
[33] ggplot2_3.3.3
