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Microarray Uniformity (2-color only)
The QC Report has two metrics that measure the uniformity
of replicated log ratios and that indicate the span of log
ratios: average S/N and AbsAvgLogRatio. These are
calculated from inlier features of replicated non-control and
spike-in probes.
For example, some microarrays have 100 different
non-control probe sequences with 10 replicate features each.
For each replicate probe, the average and SD of the log
ratios are calculated. The signal to noise (S/N) of the log
ratio for each probe is calculated as the absolute of the
average of the log ratios divided by the SD of the log ratios.
From the population of 100 S/N’s, for example, the average
S/N is determined and shown in the table below.
The second metric, AbsAvgLogRatio, indicates the amount of
differential expression (up-regulated or down-regulated). As
described above, averages of log ratios are calculated for
each replicated probe. The absolute of these averages is
determined next. Then, the average of these absolute of
averages is calculated to get a single value for the QC
Report. The larger this value, the more differential
expression is present.
Figure 20
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QC Report—Array Uniformity: LogRatios
Feature Extraction for CytoGenomics Reference Guide