Changed some comments that were understood by cylon-x as statements about licenses.

05-Get_DEGs/get_DEGs.R

@@ -85,7 +85,7 @@ for (i in seq_len(length(config$datasets))) {
 
     # Annotate the eset with gene information for better outputs.
     # First, we collect raw the gene annotations and we have two options
-    # either from the Bioconductor package or from the processed GPL file.
+    # either from the Bioconductor package or from the processed GEO plateform annotation file.
     platform_config <- get_platform(config, dataset$array_type)
 
     # We enrich the probe identifiers with the corresponding gene names using

07-Enrichment/gender_specific_pathways.R

@@ -138,7 +138,7 @@ for (i in seq_len(length(config$integrations))) {
   rm(M_filename, F_filename, M_data, F_data)
 
   #
-  # GO-CC by CP
+  # GO-CellularComponent by CP
   #
   M_filename <- paste0(output_data_dir, "CP_", male_prefix, "max-avg_gs_pivalue_gsea_GOCC.tsv")
   F_filename <- paste0(output_data_dir, "CP_", female_prefix, "max-avg_gs_pivalue_gsea_GOCC.tsv")

07-Enrichment/pathways_with_gender_specific_genes.R

@@ -146,7 +146,7 @@ for (i in seq_len(length(config$integrations))) {
   rm(M_filename, F_filename, M_data, F_data)
 
   #
-  # GO-CC by CP
+  # GO-CellularComponent by CP
   #
   M_filename <- paste0(output_data_dir, "CP_", male_prefix, "max-avg_all_pivalue_gsea_GOCC.tsv")
   F_filename <- paste0(output_data_dir, "CP_", female_prefix, "max-avg_all_pivalue_gsea_GOCC.tsv")