This is equivalent to a bootstrap p-value of 0.001.
We compared our theoretical p-values with bootstrap p-values on a block of 100 SNPs chosen from chromosome 1 (mimicking a fine-mapping association study).
In the context of resampling plans, n is the number of replicates and p is the bootstrap or jackknife support value (bootstrap percentage or bootstrap p value) expressed as a fraction of 1, i.e., the proportion of replicates that yielded a tree containing a particular phylogenetic group.
For each model, a bootstrap p value greater than 0.1 was considered indicative of a good fit with the observed data.
Table 1 lists the values of each threshold estimated by profile likelihood or least squares, their 95% confidence intervals (CIs) obtained by bootstrap, p-values for test for threshold and goodness-of-fit, and relative risk with CIs.
aThe bootstrapped p-value of the likelihood-ratio statistic indicates if the model-based estimated frequencies are of sufficient agreement to observed frequencies, i.e. the extent to which the model fits the data, with p < 0.05 indicating a poor fit.
The bootstrapped P value, 0.047, for the test of no correlation is simply the fraction of bootstrap correlations greater than 0.627, the observed value of correlation.
Although there are many ways to use the bootstrap for hypothesis testing, the method of Walters and Campbell 42 for computing a bootstrap p-value corresponding to the observed value of a test statistic T was used.
These shortlisted transcripts were further assessed using several strategies including; i) visual inspection of histograms on a gene by gene basis (an R script used to generate these is given in Additional File 4); ii) evaluation of the associated bootstrap p-values obtained during clustering and iii) consideration of additional information of biomedical interest.
By increasing the number of bootstrap replicates, one can obtain a more reliable measure of the variance of the phylogenetic bootstrap p-value [10].
