This is a test version of Biostars. For the public version, visit https://www.biostars.org.
clusterProfiler GSEA pvaluecutoff does not work?

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
r

Hello ansonkn!

We believe that this post does not fit the main topic of this site.

This question belongs on https://support.bioconductor.org/

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

0 answers

No answers yet.

Log in to answer this question.