This file is only generated when there are more than 2 conditions. It defines all possible expression patterns over the conditions using a matrix with names. Each row of the matrix refers to a different expression pattern and each column gives the expression status of a different condition. Two conditions are equally expressed if and only if their statuses are the same.
+=item B<output_file.condmeans>
+
+This file is only generated when there are more than 2 conditions. It gives the normalized mean count value for each gene/transcript at each condition. It is formatted as a matrix with names. Each row represents a gene/transcript and each column represent a condition. The order of genes/transcripts is the same as 'output_file'. This file can be used to calculate fold changes between conditions which users are interested in.
+
=back
=head1 EXAMPLES
rsem-run-ebseq GeneMat 3,4,4 GeneMat.results
-Two files, 'GeneMat.results' and 'GeneMat.results.pattern', will be generated.
+Three files, 'GeneMat.results', 'GeneMat.results.pattern', and 'GeneMat.results.condmeans', will be generated.
=cut