Table 1.

Assessment results:

Platform	Preprocessing	Slope (SD)	SD	99%	SNR	TOP	NA%
Illumina	QN	0.56 (1.02)	0.15	0.88	3.73	0.38	0
Exiqon	QN	0.52 (0.75)	0.14	0.98	3.71	0.27	0
Ambion	QN	0.97 (0.75)	0.27	1.91	3.59	0.17	0
Agilent	Default	1.12 (0.66)	0.32	1.91	3.50	0.11	14.63
Illumina	BGC & QN	0.61 (1.11)	0.18	1.45	3.39	0.22	0
Illumina	Default	0.60 (1.15)	0.24	2.55	2.5	0.04	4.89
Ambion	BGC & QN	1.20 (1.55)	0.55	4.02	2.18	0.03	0
Exiqon	BGC & QN	1.02 (1.02)	0.47	2.97	2.17	0.03	0
Ambion	Default	1.12 (1.34)	0.55	3.92	2.04	0.02	0

For each platform, we report summary assessments for accuracy, precision, and overall performance. The first column shows the signal detection slope which can be interpreted as the expected observed difference when the true difference is a fold change of 2. In parenthesis is the standard deviation of the log-ratios associated with non-zero nominal log-ratios. The second column shows the standard deviation (SD) of the log-ratio null distribution. The SD can be interpreted as the expected range of observed log-ratios for genes that are not differentially expressed. The third column shows the 99th percentile of this null distribution. It can be interpreted as the expected minimum value that the top 1% of non-differentially expressed miRNA will reach. The fourth column shows the ratio of the values in column 1 and column 2. It is a rough measure of signal to noise ratio. The fifth column shows the probability that, when comparing two samples, a gene with true log fold change of 2 will appear in a list of the top 1% genes with the highest log-ratios. The sixth column shows the percentage of negative values in the default data set.