Quantification of EGFP florescence was performed on 50 μm×50 μm regions of interest (ROI) in the tail region, using the maximum pixel counting utility.
Among the filter types considered here, we have found that filters using the maximum normalized count appear to be best able to correctly filter genes with low levels of expression and little evidence of differential expression.
To take into account phylogenetic uncertainty, reconstructions were performed on 1000 trees from the stationary Bayesian tree sample, using the Maximum Parsimony criterion and counting all trees with uniquely best states.
This same order was also observed in terms of overall selection pressure, measured as the mean ratio of nonsynonymous (dN) to synonymous substitutions (dS) per site (dN/dS), estimated using the maximum likelihood SLAC (Single Likelihood Ancestor Counting; http://www.datamonkey.org/) method [24]: N = 0.048; L = 0.055; M = 0.078; G = 0.119; P = 0.187.
To do this, we simulated 1,000 data sets on Tree-10 using the maximum likelihood values for the root count, λ and μ calculated under the duplication model.
The maximum counts per pixel per minute were obtained from the ROIs and were converted to counts per milliliter per minute using a calibration constant.
c is the maximum counts charged in the folder.
Where: i is the maximum counts charged in the folder.
The model was fit using the maximum-likelihood procedure implemented in Count, with the default null model as a starting point, and with gain, loss, and duplicate rates estimated for all branches of the tree.
I compared citation counts for the 219 publications listed in both databases (60% of the total sample), and consistently used the maximum value when citation counts differed (100 publications, 46% of subsample).
