I am running EdgeR as a part of a bigger pipeline (CAP-miRSeq to be precise) where I quantify the expression and differential expression of miRNAs. However, the values in differential_expression tables does not match (though they are usually close) with values in expression tables (miRNA_expression_norm.xls, mature_miRNA_expression.xls and miRNA_expression_raw.xls). I am not sure which read count value were used in the differential expression tables.
Does EdgeR also calculate the read count first before doing differential expression calculations? There is another tool in the big pipeline which has the capabilities to calculate read count. But I am not sure if the read counts come from that tool or from EdgeR.
Can you please tell me where what could be the reason for different numbers in expression and differential expression tables?