conf.txt

[SETTINGS]
#General options
#set the folder name contains study files
study_dir = demo_user/studies/



plots = YES
#Annotation - Define Classes
controls = 0
cases = 1
#only for Multivariate Analysis
cases2 = 2

#GISU Options
RUN_GISU = NO
#if YES load data from web, if NO load local data from folder data/
gene_data_online = YES
#mean, min, max
# If NO, load platforms
updated_genes = YES
transformation_method = mean
#Platform name for file. For multiple study files insert a list of platforms separated by comma (,) one per study
platform = GPL201,GPL4191,GPL6947,GPL570,GPL6244,GPL570,GPL6244,GPL571,GPL6244,GPL17077,GPL339,GPL96,GPL571
gene_history_file = data/Gene_History_Reference/gene_history.txt
homo_sapiens_file = data/Homo_Sapiens_reference/homo_sapiens_gene.txt
platforms_folder = data/Platforms/

#Meta - Analysis Options

#Run a meta-analysis giving only Effect Sizes and Standard Errors (YES or NO)
run_simple_meta_analysis = NO


bootstrap = NO
num_of_reps = 200
#Level of Significance of Mulitple Comparisons
significance_level = 0.01
#one_step , step_down, step_up, all
multiple_comparisons = all

#Multivariate Analysis Options
multivariate = NO
#bonferroni, sidak, holm, holland, hochberg, simes, none
venn_correction = bonferroni
#Choices = global1_RE, global1_stoufer, global1_stoufer_weighted , global1_p_fisher,  global1_p_edg1  global1_p_edg2, global2
venn_choice = global1_stoufer_weighted
alpha = 0.05
# Multiple_tests choices = one_step , step_down, step_up, none
multiple_tests = one_step

#Enrichment Analysis Options
enrichment_analysis = NO
organism = hsapiens
threshold = 0.05
#Default 'fdr'. Other options are 'bonferroni' and 'g_SCS'
threshold_method = fdr


#Bayesian Meta-analysis
bayesian_meta_analysis = NO
#parameters for bayesian_meta_analysis
a = 0
b = 2