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I am running basic gseGO on my deg data. I've followed this exact code with no issues before. Now, however, I am getting plots where the adjusted p value is the same for all enriched terms. This seems wrong, and I can't figure out where this problem rises from. Is it possible to have the same p.adjust values for many terms?
#Rank gene with t.statistics:
#first make sure to get rid of duplicates:
GLDSdds_resDF<- as.data.frame(GLDSdds_res)
GLDSdds_resNODup<- GLDSdds_resDF %>% group_by(SYMBOL) %>% summarise(stat = mean(stat, na.rm = TRUE))
#then make a sorted Rankgene for later use as a geneList:
Rankgene_GLDS420<- GLDSdds_resNODup$stat
names(Rankgene_GLDS420)<- GLDSdds_resNODup$SYMBOL
sorted_RankgeneGLDS420 <- Rankgene_GLDS420[order(Rankgene_GLDS420, decreasing = TRUE)]
#converting ranked gene data frames into compatible geneLists for gseGO
geneList.GLDS420 <- sorted_RankgeneGLDS420
####GO Gene Set Enrichment Analysis (set.seed(123) & gseGO(seed = TRUE))
set.seed(1234)
goGLDS420.gsea <- gseGO(geneList = geneList.GLDS420,
OrgDb = org.Mm.eg.db,
seed = TRUE,
ont = "ALL",
keyType = "SYMBOL",
minGSSize = 50,
maxGSSize = 1000,
pvalueCutoff = 0.05,)
goGLDS420.gsea@result
# RESULTS: #
NES pvalue p.adjust qvalue rank leading_edge
GO:0098800 -2.661837 1e-10 2.906542e-09 1.370389e-09 4815 tags=52%, list=20%, signal=41%
GO:0005746 -2.650916 1e-10 2.906542e-09 1.370389e-09 5402 tags=60%, list=23%, signal=47%
GO:0019646 -2.581905 1e-10 2.906542e-09 1.370389e-09 5402 tags=64%, list=23%, signal=50%
GO:0015986 -2.577351 1e-10 2.906542e-09 1.370389e-09 5556 tags=63%, list=24%, signal=48%
GO:0098798 -2.552119 1e-10 2.906542e-09 1.370389e-09 5429 tags=49%, list=23%, signal=39%
GO:0070469 -2.537042 1e-10 2.906542e-09 1.370389e-09 4645 tags=52%, list=20%, signal=42%
GO:0006119 -2.505556 1e-10 2.906542e-09 1.370389e-09 5429 tags=53%, list=23%, signal=41%
GO:0048762 2.486006 1e-10 2.906542e-09 1.370389e-09 2766 tags=34%, list=12%, signal=30%
GO:0060485 2.469346 1e-10 2.906542e-09 1.370389e-09 2766 tags=33%, list=12%, signal=30%
GO:0007179 2.455608 1e-10 2.906542e-09 1.370389e-09 4458 tags=42%, list=19%, signal=34%
GO:0071559 2.435177 1e-10 2.906542e-09 1.370389e-09 4458 tags=41%, list=19%, signal=33%
GO:1903844 2.428603 1e-10 2.906542e-09 1.370389e-09 3029 tags=36%, list=13%, signal=32%
GO:0090287 2.406678 1e-10 2.906542e-09 1.370389e-09 4732 tags=41%, list=20%, signal=33%
GO:0071560 2.391128 1e-10 2.906542e-09 1.370389e-09 4458 tags=40%, list=19%, signal=33%
GO:0017015 2.388548 1e-10 2.906542e-09 1.370389e-09 3029 tags=35%, list=13%, signal=31%
GO:0001837 2.338641 1e-10 2.906542e-09 1.370389e-09 2612 tags=32%, list=11%, signal=29%
GO:0007178 2.335834 1e-10 2.906542e-09 1.370389e-09 4509 tags=38%, list=19%, signal=31%
GO:0090092 2.316196 1e-10 2.906542e-09 1.370389e-09 4451 tags=39%, list=19%, signal=32%
GO:0009060 -2.308490 1e-10 2.906542e-09 1.370389e-09 4736 tags=45%, list=20%, signal=37%
GO:0000775 -2.295537 1e-10 2.906542e-09 1.370389e-09 5115 tags=44%, list=22%, signal=35%
sessionInfo( )
