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To confirm that the binding sequence results were not dependent on the particulars of the thresholds chosen, we chose a stringent threshold of 10.6 for the enrichment scores as well as a more lenient value of 10.0 (Supplemental Figure 4).
One strategy is to be fairly flexible in the first step using a p-value of 0.5 and apply a strict variable inclusion frequency level of 90% in step 2. Another strategy is to be strict in step 1 (e.g. take a p-value of 0.157 or 0.05) and take a more lenient value at step 2 (e.g. 70%).
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To test our hypothesis of IFC underactivation, we reanalyzed the data at a more lenient p value of p <.002 for voxelwise comparison.
For massive-testing platforms, such as genome-wide association studies, it might be expected that many false-positive violations of HWE would occur if a lenient P value threshold were set.
All findings remained significant at a more lenient P-value (P < 0.03).
While using lenient P-value thresholds might well improve the overlap, it might also produce many false positives.
The BLAST step was performed with a lenient E-value cutoff at 0.1 to account for the high sequence variability among the olfactory gene families.
Cmsearch was performed against a custom sequence database described above using a lenient e-value cut-off of 1.0 (cmsearch –E 1.0 –mid –cpu 4).
Therefore, we used a more lenient P-value threshold for prioritization and annotation of a set of 'promising' SNPs, reported estimates of variance explained by all GWAS SNPs and made available the complete set of our GWAS results.
The mapping step was done using default settings, whereas a lenient E-value (0.1) and lower annotation cut-off (55) and GO-weight (5) were used in the first annotation step to increase the proportion of annotated transcripts.
Because of the small sample size, we used a lenient P-value of 0.01 as a threshold for our analysis and found 105, 59, and 89 QTTs associated with state 3, state 4, and P O ratio, respectively, in the analysis averaged across sexes (see Additional file 3).
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