Although a threshold of 6 is recommended in the instruction manual, we used a conservative threshold of 10 because visual inspection of the array plots led to the rejection of several aberrations called using the lower threshold.
Finally, the statistical analyses, with the exception of GSEA, were performed using R software [ 48] (http://www.r-project.org), and the array plot (heat map) of the gene categories was constructed using Mathematica 8 (Wolfram Research).
Each nested plot is a 2-dimensional array of plots, each of which represents the form of a set of model solutions with a pair of distinct parameter value.
Judging from comparisons of array-specific MA-plots (results not shown) as well as array-averaged plots of expression ratio versus signal intensity (supplementary fig. 1, Supplementary Material online), we believe that the PTL normalization and normexp background correction is a better treatment of these data than VSN for removing dye bias and other artifacts present in the data.
To detect poorly performing samples in Illumina arrays, diagnostic plots of control probes in GenomeStudio are often used (Bibikova et al, 2011), and the R-package HumMethQCReport (Mancuso et al, 2011) also provides these plots.
For example, in case 24, the whole-genome array plot depicts a copy number loss of the entire X chromosome plus a suspicion of a ring X chromosome (Supplementary Figure 3A).
The image array plot (Figure 2C) clearly shows the overall differential effects of tumor growth.
By using the constrained-mode analysis, theoretical stability boundaries are obtained and compared with experimental data from similar cylinder arrays, plotted in terms of the critical reduced flow velocity versus the mass-damping parameter.
Groundwater samples define linear arrays on bivariate plots of these elements that most likely represent mixing between saline and dilute endmembers (Fig. 5).
Histograms of density versus t-value were generated for each category to observe the distribution of genes of a specific category compared with the normal distribution of all the categories on the arrays.. Plots of t-values vs. A-values were created to identify the genes in each category and observe their distribution across the array.
