search

hbc / bcbioRNASeq

R package for bcbio RNA-seq analysis.
https://bioinformatics.sph.harvard.edu/bcbioRNASeq
GNU Affero General Public License v3.0
58 stars 21 forks source link

KEGG plots fail in Funcitonal analysis template #97

Closed jnhutchinson closed 6 years ago

jnhutchinson commented 6 years ago

pathview command is running on lfc_vec and not entrez_lfc_vec

mjsteinbaugh commented 6 years ago

Thanks John I'll look into this. We need to add the FA template to our automated build checks.

hliu2016 commented 6 years ago

@mjsteinbaugh The gseKEGG function always return 0 obs. Could you check if the input parameter entrez_lfc_vec is correctly set?

mjsteinbaugh commented 6 years ago

Hi @hliu2016 I'm working on adding automatic unit testing to our functional analysis code and will push a fix for this soon.

mjsteinbaugh commented 6 years ago

This should be fixed in the latest bcbioRNASeq release (v0.2.4).