Rationale for decreasing order only in GSEA

[Nelson-Gon]

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Describe you issue

In performing GSEA, it seems the default is to have the genes sorted in decreasing order:

DOSE:::is.sorted
function (x, decreasing = TRUE) 
{
    all(sort(x, decreasing = decreasing) == x)
}

However, per the original paper, it seems the order should not matter i.e. whether ascending or descending. I would like to know if it is possible to support a non-decreasing sorted gene list or perhaps what the rationale is for a decreasing only gene sort.

This could be related to YuLab-SMU/clusterProfiler#214, YuLab-SMU/clusterProfiler#91, and YuLab-SMU/clusterProfiler#48.

Thank you,

NelsonGon

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[huerqiang]

It must be descending in DOSE.

[Nelson-Gon]

It must be descending in DOSE.

I set by to fgsea but still cannot sort by ascending order. Is fgsea also using only descending order?

[shanshenbing]

Hello, I use GSEA function from clusterprofiler following the tutorial: http://yulab-smu.top/biomedical-knowledge-mining-book/universal-api.html. The tutorial works well. When I run my data, I got warnings same as YuLab-SMU/clusterProfiler#214. The issue tells me that I should use rank rather than log2fc, which may have the same values and cause warnings. Actually, when I use rank to run GSEA() fun, I got another warning: "unbalanced (positive and negative) gene-level statistic values" and the warning told me that I could use scoreType = "pos" to run GSEA. After using this para, I found these results were not the same, especially between em2 and gl_df.
Here is my code.

library(tidyverse)
library(clusterProfiler)

data(geneList, package="DOSE")
head(geneList)

m_t2g <-msigdbr::msigdbr(species = "Homo sapiens", category = "C2") %>%
dplyr::select(gs_name, entrez_gene)
em2 <- GSEA(geneList, TERM2GENE = m_t2g)
head(em2)
dotplot(em2)

gl_df <- data.frame(gene=names(geneList),
log2fc = geneList)
gl_df <- gl_df %>% dplyr::mutate(rank= rank(log2fc, ties.method = 'random')) %>% arrange(desc(rank))

gl <- gl_df$rank
names(gl) <- gl_df$gene
head(gl)
em2_gl <- GSEA(gl, TERM2GENE = m_t2g)

dotplot(em2_gl)

em2_gl2 <- GSEA(gl, TERM2GENE = m_t2g, scoreType = "pos")
dotplot(em2_gl2)

plot from em2:

plot from em2_gl:

plot from em2_gl2:

I do not think this is normal. At present, I use a compromised method to solve this problem.
Here is my code.
dplyr::mutate(rank = rank(avg_log2FC, ties.method = "random"),
avg_log2FC=avg_log2FC + rank*(1e-15)) %>%
arrange(desc(avg_log2FC))
add a small value to every log2FC to make the value is unique.

Hope you share more help or information.
Thank you!

[huerqiang]

@shanshenbing This warning has no effect on the accuracy of the results.