Only transcripts that were assigned to a present call at two sequential time points in at least one time series were retained for further analysis.
We used treatment as a fixed effect and introduced an error term for the two sequential time-points when each population was sampled.
Particles with similar XY coordinates (XY distance was less than the radius of the smaller of the two particles) present in at least two sequential time points were classified as a single object.
Thus each mode represented the sign of the rate of expression change between two sequential time points.
The waves of CYP expression occurred with different clusters expressed most strongly usually only at one or two sequential time points (i.e., unimodally) during development.
Drift is less of a problem when summing over long periods of time, since it is only pulses of activity near the end of the time period that may be incorrectly attributed to one of the two sequential time periods.
To compare gene expression profiles between two sequential time-point samples, the edgeR package (http://www.bioconductor.org/packages/2.3/bioc/html/edgeR.html) was used to adjust for differences in library size and therefore raw read counts per gene (or per tag) were directly used as input.
The data extracted from the images was then processed using the web application described by den Hertog et al.[ 3] to identify particles with equivalent XY coordinates present in at least two sequential time points.
Forty RA patients received high-resolution peripheral quantitative computed tomography (HR-pQCT) analysis of the metacarpophalangeal joints II and III of the dominantly affected hand at two sequential time points (baseline, one year follow-up).
Upon the completion of staining, the arrays were washed three sequential times in fresh 1 × TNT (1 M Tris-HCL, pH 7.6, 5 M NaCl, Tween-20, and milli-Q water) and then washed two final times in fresh solutions of 0.05% Tween-20 and 0.1 × SSC with gentle agitation.
Through analytic manipulation, the split semi-implicit method breaks the full matrix time advance into four sequential time advances, each involving smaller matrices.
