Usage:
- rsem-find-DE data_matrix_file [--ngvector ngvector_file] number_sample_condition1 FDR_rate output_file
+ 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_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.
+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.
differential expression analysis.
We thank earonesty for contributing patches.
+
We thank Han Lin for suggesting possible fixes.
## <a name="license"></a> License
projects / rsem.git / blobdiff