The statistical tests combined are ordinary fold changes, ordinary t-statistics, SAM (significance analysis for microarrays) statistics and moderated t-statistics.
All microarray statistics including t-test and analysis of variance (ANOVA) with permutation analysis (n = 1000) and cluster analysis were performed using the SUMO software package [25] [27].
Differential expression analysis was performed using the Bioconductor package SAMR, which implements SAM (Significance analysis of microarray) statistics in R [ 12], and a cut-off of 5% false discovery rate (FDR) was applied.
Microarray statistics including the common genes (2891) of S. cerevisiae and P. pastoris.
PV indicates the p-value obtained using either ANOVA or microarray statistics.
Microarray statistics including all genes that passed the adjusted p-value threshold (p-value ≤ 0.05).
Pawitan et al. 2005 notes the need for multiple testing by FDR in their analysis of microarray statistics, noting that using a p-value solely in data cleaning can result in low sensitivity.
At a first glance, the microarray statistics (see Table 2) of the approximately 3900 annotated sequences for P. pastoris displayed more than 600 genes, independent of the strain, that were differently regulated (adjusted p-value ≤ 0.05) when comparing normoxic and hypoxic conditions.
