addMotifAnnotation() returned Null motifEnrichmentTable

[pchiang5]

Hellow,

When tried to run the code by the following tutorial: https://bioconductor.org/packages/release/bioc/vignettes/RcisTarget/inst/doc/RcisTarget_MainTutorial.html

The first step ran correctly

# 1. Calculate AUC
motifs_AUC <- calcAUC(geneLists, motifRankings)

with the output

> motifs_AUC

AUC for 1 gene-sets and 24453 motifs.

AUC matrix preview: jasparMA1023.1 geneListName 0.01503321 taipale_cyt_methIRX3_NACGYRNNNNNNYGCGTN_eDBD_meth geneListName 0.01503321 taipaleDBP_DBD_NRTTACGTAAYN cisbpM4240 scertf__macisaac.ACE2 geneListName 0.01503321 0.01503321 0.01503321

However, step 2 below returned an empty table

# 2. Select significant motifs, add TF annotation & format as table
motifEnrichmentTable <- addMotifAnnotation(motifs_AUC,       motifAnnot=motifAnnotations_hgnc)
> motifEnrichmentTable

Null data.table (0 rows and 0 cols)

the motif features in the test file "hg19-tss-centered-10kb-7species.mc9nr.feather" did match the annotations obtained with the following code:

# Motif-TF annotations
data("motifAnnotations_hgnc")
motifAnnotation <- motifAnnotations_hgnc

The problem remained even I tried to specify the motif name with 'idColumn = "motif"'.

How shall I address the error at this step? Thanks

[pchiang5]

I found the empty output was because I use all genes (>20,000 genes) as geneLists. Reducing the gene number in the list worked fine.