Figure 18

Plot of gene with a possibly ambiguous differential expression status. In this paper we point out the need to establish truth at the probe set/CEL file level as well as at the spike-in level. Achieving that goal will require community-wide consensus as to what constitutes differential expression, based on the contents of the probe sets involved in the comparison. For some genes consensus might not be an easy thing to achieve, as this plot of 1552_i_at from the HG-U95A experiment suggests. HG-U95A experimental condition Q is plotted in red, and condition A in cyan. Even though all summary measures considered in this paper declare this gene to be highly differentially expressed, it would not be at all surprising to find many opinions as to whether this gene is really expressed or not. Just as "Marginal" is an acceptable condition when making MAS 5 calls, so "Ambiguous" may have to be an acceptable state for some comparisons.