At this very conservative threshold differential expression of other genes was not significant.
Thus, we selected a four-fold change as a conservative criterion for differential expression.
This procedure commonly yields dispersion estimates that are higher than with replicated treatments, resulting in a more conservative estimate of differential expression.
For these cases, we used a conservative test of differential expression (see Methods).> We confirmed enhanced expression of E-Cadherin (CDH1), E47-like factor 3 (ELF3), Mitogen Activated Protein Kinase 4 (Mand4) and Podocalyxin (PODXL).
Whilst it is difficult make direct comparisons between their p-values, the lower p-value required to achieve maximal correspondence with edgeR compared to AC suggests that edgeR, used with the parameters given in Methods, is more conservative in its differential expression calls.
A 5-fold difference in FPKM values was used as a conservative criterion for significant differential expression.
For the cDNA data, conservative threshold values for differential expression were chosen to minimize the false-positive and false-negative rates estimated from Scorecard control probes printed on the arrays.
While this range may exclude some rare, low-abundant transcripts, it presents a more conservative and reliable approach to differential expression testing by emphasising the accuracy of the assembly rather than the identification of low-abundant transcripts from both treatments.
Using a conservative analytical approach to identify differential expression of individual seminal fluid components, at least seven of 31 secreted seminal fluid proteins examined showed consistent differences in relative abundance under high versus low sperm competition conditions.
But, to be more conservative, and to try to get only differential expression due to breeds and not merely to stochastic reasons, we extracted differentially expressed genes from breed effects data, with absolute z score threshold > 1.65.
