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.
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.
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.
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.
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).
Various hemodynamic parameters were measured using direct pressure signals and continuous arterial waveform analysis at three sequential time points: before, during and after hyperoxia.
All measurements were performed with patients in supine position at three sequential time points: pre-intervention, during intervention and post-intervention.
Five sequential time points were chosen for testing: days 1 (24 hours after seeding), 3, 5, 7 and 9.
These networks map all detectable coexpression relationships occurring at each of three sequential time points over the course of letrozole treatment enabling us to track how the network is rewired as it adapts to the presence of the drug.
