For replicate subject-level observations, we expect the intra-cluster correlation (ICC) to be moderate to high, while for other types of clustered data, the ICC can be quite low.
Having obtained point estimates for all the genes, studies of differential expression between pairs of phenotypes are carried out by comparing the collections of point estimates under the phenotypes, using a t-type statistic such as in SAM [73], Cyber-T [74] or Limma [75], all of which rely on the availability of replicate subjects in each phenotypic condition, for estimation of variances.
Total RNA was independently extracted for each biological replicate, subjected to polyA+ or ribosomal RNA depleted total RNA (RZ) enrichment protocols, quality-controlled, pooled and converted into complementary DNA sequencing libraries for the Illumina Genome Analyzer platform (Additional file 1: Table S1, see Materials and methods).
Moreover, both repositories present some replicated subject sampled in different dates (same person pictured in different years).
All assessors were unaware of presentation designs, the presence of technical replicates, subject ages and age ranges.
Bootstrap values were determined from 1,000 replicates subject to full heuristic searches with simple addition sequence and NNI branch swapping to provide measures of relative clade support.
DamID chromatin profiles were generated and biological replicates subjected to a series of analyses to establish statistically significant data sets for each individual experiment [ 22].
In this novel formulism, we have addressed data variability in biological systems by integrating network identification with the bootstrap resampling technique, hence predicting robust interactions from limited experimental replicates subjected to noise.
Sera were obtained from 38 (30 cancer and 8 control) subjects, fractionated, and analyzed by MALDI-TOF MS. We obtained 507 spectra with the following numbers of replicates per subject: 28 subjects had 12 replicates; 5 subjects had 24 replicates; 4 subjects had 11 replicates; and 1 subject had only 7 replicates.
The five replicate were subject to estimate the intra-day and inter-day precision.
Because RF++ is constructed to accommodate clustered data, it summarizes classification both at the replicate and subject level.
