Because there is typically large between array variation, information about the association will come from the differences in traits and expression measurements between the two values hybridised to the two dyes on the same array.
In other words, based on the same array configuration and the same number of sensors, the proposed algorithm has twice larger array aperture than the compared FOC-TMR algorithm in [26].
Every sample was run in duplicate on the same array for each gene.
All probe set values were normalized to the 5th percentile value of all probe sets on the same array.
When available, matching normal DNA was also analysed on the same array platform and in the same batch.
Parallel experiments on the same array design were conducted, with and without addition of COT-1 DNA.
Normalized values were used to calculate B-statistics, which were analyzed with allowance for the correlation between adjacent duplicate spots printed on the same array.
We ran the P/A call algorithm on all arrays and examined the consistency of P/A calls between redundant probe sets on the same array.
We determined the genes differentially expressed in the ovarian cancer cases examined in Tothill et al. [16] by comparing the expression profiles to data from ovarian surface epithelium brushings pooled from ten patients generated on the same array platform [14].
Considering relative fluorescence (such as a log-ratio), particularly to a common reference such as a cell line reference hybridized on the same array, provides a robust normalization technique to control for such manufacturing variability [22].
Technical replicates on the same array were combined.
