it seems there is an inconsistency between the documentation and what's in the snakefile for the statistical tests at the gene level; the choice of test is ambiguous if the gene_diff_method is not specified in the configuration file.
in the documentation:
gene_diff_method: Method used for gene differential testing (default: 'DESeq2' or 'limma-voom' if number of samples > 100). Possible choices are 'DESeq2' and 'limma-voom'. 'limma-voom' is a faster alternative for large cohorts.
in the snakemake file (lines 169-174):
AUTOMATICALLY SET GENE DIFF METHOD TO LIMMA-VOOM IF MORE THAN 100 SAMPLES
if 'gene_diff_method' not in config :
if len(SAMPLE_NAMES) >= 100:
GENE_DIFF_METH = "DESeq2"
else:
GENE_DIFF_METH = "limma-voom"
it seems there is an inconsistency between the documentation and what's in the snakefile for the statistical tests at the gene level; the choice of test is ambiguous if the gene_diff_method is not specified in the configuration file.
in the documentation: gene_diff_method: Method used for gene differential testing (default: 'DESeq2' or 'limma-voom' if number of samples > 100). Possible choices are 'DESeq2' and 'limma-voom'. 'limma-voom' is a faster alternative for large cohorts.
in the snakemake file (lines 169-174): AUTOMATICALLY SET GENE DIFF METHOD TO LIMMA-VOOM IF MORE THAN 100 SAMPLES if 'gene_diff_method' not in config : if len(SAMPLE_NAMES) >= 100: GENE_DIFF_METH = "DESeq2" else: GENE_DIFF_METH = "limma-voom"