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The agar plates were inoculated with a replicating spot device and the inoculum was approximately 104 CFU per spot.
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Furthermore, when dealing with two-channel arrays, there are two different intensity values associated with each replicated spot.
We compute the minimum inter-spot spacing for replicate spots to enhance sensitivity.
To reduce analytical complexity, for each gene on the array we analyzed the arithmetic mean of replicated spots within arrays.
To create a null distribution for the rank correlation coefficient, replicate spots from two Mock microarrays were treated as a separate microarray by enumerating replicate spots 1, 2, 3, or 4 arbitrarily and assigning all spots with "i" to the ith array, resulting in 4 Mock arrays.
Averaging of replicate spots and determination of differential expression.
Spots with both signal-to-noise levels below 10 were removed and replicated spots were merged.
All data were averaged for replicate spots upon a slide, and then further averaged across slides.
After assessing normal distribution of replicate spots using the Kolmogorov Smirnov test, replicates were pooled by their arithmetic means.
The average correlation in intensity between these replicated spots is 0.906, where the average is taken over 62 different chips.
Values of replicate spots passing quality control were averaged and Lowess normalization of log2-expression ratios (ER) was performed.
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