The median time to improvement according to the least stringent criterion of treatment response was 3.7 weeks; the probability of improvement was estimated at 60% at or before 4 weeks and 88% at or before 12 weeks.
For all data sets, the number of alignment positions was reduced with gblocks applying least stringent selection criteria.
To assess the validity of our predictions, we selected QTL2 (on chromosome X) for experimental validation as this QTL, despite being important in both the 16% and 17% pool seemed to be one of the more difficult QTLs to detect (only confirmed by the least stringent selection criteria).
Regardless of these potential caveats, our results indicate that reliable transcriptional analysis of tumour cells isolated with the DEPArray is at least feasible if stringent criteria for RNA quality are applied.
More stringent criteria (at least ACR50/LDAS), faster onset (⩽3 months) and sustainability (>3 visits) of ACR50/LDAS best reflected patient satisfaction (positive LR >10).
We analyzed further the set of 118 human pre-miRs that completely contained at least one conserved TFBS using stringent criteria (z-score ≥ 2.33, p < 0.01; Figure 2, Additional Files 1 and 2).
Finally, the new repeats were blasted against the HSY and the corresponding X sequences using Standalone BLAST software (NCBI) and screened based on the following more stringent criteria: 1) at least a 50% alignment over a consensus sequence, 2) occurrence of at least 10 times, and 3) an aligned region with at least 100 bp and > 75% identity.
Applying the less stringent criteria of at least 3 positive measurements among the 6 combined measurements of both markers, 1 of 22 healthy controls was classified as positive (5%), whereas 18 of 49 patients with polyps (37%) and, again, 3 of 5 cancer patients were found to be positive.
We determined significant myogenic hypermethylation or hypomethylation using stringent criteria, namely, at least a 50% difference in methylation in Mb and Mt (as a set, MbMt) vs. the nonmyogenic cell cultures or in skeletal muscle tissue vs. nonmuscle tissue at a significance level of P < 0.01 using fitted binomial regression models at each monitored CpG site [ 11].
When determining the presence or absence of a repeat feature, we only used the least-stringent mapping criteria.
