-before running function 'EBTest'.
-
-At last, RSEM provides a R script, 'rsem-find-DE', which run EBSeq for
-you.
-
-Usage:
-
- rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_of_samples_in_condition_1 FDR_rate output_file
-
-This script calls EBSeq to find differentially expressed genes/transcripts in two conditions.
-
-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_of_samples_in_condition_1: 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.