We will report on the quality of the array as a whole as defined by the overall microarray signal to noise ratio and reproducibility between array replicates.
Consistency between array replicates was assessed by comparing mean (from the two duplicates) intensity ratios for each clone.
This method allowed for "between array" normalization, which aimed to enhance the comparability of signal ranges between replicate arrays by defining the final intensity of probes within a specific quantile as the average value of this quantile.
A mixed-model approach was chosen to adequately describe between-array variation and still utilize probe-replicates (3 replicates of each probe in each array).
A mixed-model approach was chosen to adequately describe between-array variation, and utilized the probe-replicates in each array.
2. Apply quantile normalization to replicate arrays in order to facilitate between-array comparability and use the average value of each quantile as the final intensity for corresponding probes.
The bulks were compared by simultaneously assaying them on the same DArT array (replicated up to eight times) and measuring the contrast of hybridization intensity for markers that were identified as polymorphic in a comparison between the two parents on separate replicated arrays.
A further measure of qPCR accuracy and reproducibility is the variation between replicates and between different Taqman arrays.
Correlations between within-array replicate spots were integrated in the statistical model as described in [ 60].
We combined the within-array replicates on individual arrays and searched for patterns.
