I am having trouble running tmodhg with ECC library?
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Entering edit mode
4.0 years ago
biotrekker ▴ 110
ECC.gmt <- read.gmt("~/Desktop/Research/Tools_and_Databases/gmtfiles/ENCODE_and_ChEA_Consensus_TFs_from_ChIP-X.gmt")

#-------------------------------------------------------#
# Hypergeometric Enrichment
# create a character vector of DEGs that are up and down - fix for your data

gene_list<-read.csv("~/Desktop/REST_TARGETS_EC.csv",header = TRUE)
#gene_list<-as.character(gene_list)
gene_list<-gene_list$Gene

# Create all gene
# create a character vector of *all* genes found in the comparison
all_genes <- unique(as.character(efit$genes$Symbol))
# length of up and down genes
length(gene_list)
length(all_genes)
# Run hypergeometric test with tmod
tmodHG_result <- tmodHGtest(gene_list, all_genes, mset = ECC.gmt)

I get this error:

tmodHG_result <- tmodHGtest(gene_list, all_genes, mset = ECC.gmt)
Error in .mset_sanity_check(mset, modules) :   Required members missing from the list mset parameter

What should I do?

Thanks!

tmodhg microarray analysis • 798 views
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