Hello, I find that some transcripts found by EBSeq have a problematic pattern in the raw data, where only one sample has any counts. For example, in a 3 vs. 3 scenario, these are some of the transcripts which have posterior probability of D.E. = 1 : Sample13 Sample14 Sample15 Sample16 Sample17 Sample18 comp209187_c0_seq13 0.00 112.99 107.04 0.00 0.00 0.00 comp209188_c11_seq1 40.00 38.91 42.89 107.00 155.96 105.58 comp209189_c8_seq1 248.02 235.06 287.10 18.82 93.13 10.74 comp5876_c0_seq1 0.00 0.00 0.00 128.00 0.00 0.00 comp701657_c0_seq1 0.00 0.00 0.00 187.00 0.00 0.00 comp85095_c0_seq1 0.00 0.00 0.00 125.01 3.00 0.00 The first 3 samples are in one condition, the last 3 are in the other condition. The values are expected counts from RSEM, which the journal article says EBSeq works with. I'm a bit cautious about claiming the last 3 transcripts are D.E. Is there anything in EBSeq analogous to the new EdgeR-Robust algorithm which can deal with these observations ? -------------------------------------- Dario Strbenac PhD Student University of Sydney Camperdown NSW 2050 Australia