-data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.
-[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.
-number_sample_condition1: the number of samples in condition 1. A condition's samples must be adjacent. The left group of samples are defined as condition 1.
-FDR_rate: false discovery rate.
-output_file: the output file.
+data_matrix_file: m by n matrix containing expected counts, m is the number of transcripts/genes, n is the number of total samples.
+[--ngvector ngvector_file]: optional field. 'ngvector_file' is calculated by 'rsem-generate-ngvector'. Having this field is recommended for transcript data.
+number_sample_condition1: the number of samples in condition 1. A condition's samples must be adjacent. The left group of samples are defined as condition 1.
+FDR_rate: false discovery rate.
+output_file: the output file. Three files will be generated: 'output_file', 'output_file.hard_threshold' and 'output_file.all'. The first file reports all DE genes/transcripts using a soft threshold (calculated by crit_func in EBSeq). The second file reports all DE genes/transcripts using a hard threshold (only report if PPEE <= fdr). The third file reports all genes/transcripts. The first file is recommended to be used as DE results because it generally contains more called genes/transcripts.