If there are more than 2 different conditions among the samples, the output format is different. For differential expression analysis with more than 2 conditions, EBSeq will enumerate all possible expression patterns (on which conditions are equally expressed and which conditions are not). Suppose there are k different patterns, the first k columns of the output file give the posterior probability of each expression pattern is true. Patterns are defined in a separate file, 'output_file.pattern'. The k+1 column gives the maximum a posteriori (MAP) expression pattern for each gene/transcript. The k+2 column gives the posterior probability that not all conditions are equally expressed (column name "PPDE"). The genes/transcripts are reported in descending order of their "PPDE" column values. For details on how EBSeq works for more than 2 conditions, please refer to EBSeq's manual.
=item B<output_file.pattern>
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.
If there are more than 2 different conditions among the samples, the output format is different. For differential expression analysis with more than 2 conditions, EBSeq will enumerate all possible expression patterns (on which conditions are equally expressed and which conditions are not). Suppose there are k different patterns, the first k columns of the output file give the posterior probability of each expression pattern is true. Patterns are defined in a separate file, 'output_file.pattern'. The k+1 column gives the maximum a posteriori (MAP) expression pattern for each gene/transcript. The k+2 column gives the posterior probability that not all conditions are equally expressed (column name "PPDE"). The genes/transcripts are reported in descending order of their "PPDE" column values. For details on how EBSeq works for more than 2 conditions, please refer to EBSeq's manual.
=item B<output_file.pattern>
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.