Compared to a normal breast tissue standard (12 pooled normal breast tissues) loss of ID4 mRNA expression in unmethylated breast cancer specimens was marginal (median fold change = 1.3).
Reduction of duplicates for a given gene was done by judgement call factoring in signal intensity, P-value, distribution of calls ("Present" was judged as more reliable than "Marginal") and fold-change; only one entry per gene was retained for a total of 2231 transcripts with differential expression greater than 2-fold.
Δ fold denotes the thresholds used in the fold change approach, and p(D | M) the marginal data likelihood as computed in equation 1.
Peptidoglycan (PGN -induction resulted in marginal uPGN -inductionf SsLresultedmepoints, 6, 12 and 24 h (fold change below 1.5) and no significant change in the expression at early timarginal.
We further examined the 45 SAS pairs that were detected as either present or marginal in the 5-FU sensitive experiment; we decided not to include a fold change filter at this stage as it is not necessarily to have both the sense and the antisense transcript altered to a certain level to see a functional effect.
The gene set determined by this fold change and FDR multiplicity corrected cutoff, corresponds to a median raw marginal P-value of ∼0.00015 for the underlying T-statistics.
Probesets were selected for analysis if present or marginal in all controls or all of any of the treatments, and filtered according to fold change (>1.5-fold) with any condition (ET-1, C3T, PD184352, C3T/ET-1 or PD184352/ET-1) relatove to controls.
The absolute call (present, marginal, absent) and average difference of 22,215 gene expressions in a sample, and the absolute call difference, fold change, average difference of gene expressions between two or several samples were normalized and identified using these software.
At the very least, the authors should provide in their various tables, the enrichment fold change which is the observed number in the intersection, divided by the expected number (given fixed marginal counts for each factor) under the null hypothesis.
Marginal difference was observed in outcomes among different normalization methods, including the intra-platform reproducibility [see Additional file 5] and fold change correlation with TaqMan assays [see Additional file 6].
