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The background corrected and normalized data were then filtered by applying a false discovery rate of < 5%.
Proteins were identified using PEAKS (http://www.bioinfor.com/peaks) by applying a false discovery rate (FDR) of 1% and quantified with LC Progenesis softwarev v4.1 (Nonlinear Dynamics, Newcastle, UK).
The p values were converted to q values by applying a false discovery rate (FDR) correction to account for multiple testing and false positives (Benjamini and Hochberg 1995).
First, the global model was adjusted by the least-squared technique to identify differentially expressed genes, and significance was assessed by applying a false discovery rate (Q = 0.01).
We identified 2,758 differentially expressed probes (2,651 transcripts) by applying a false discovery rate of 0.05, associated with an absolute log2 (fold change) threshold of 1.
Differentially expressed gene lists were then generated by applying a false discovery rate (FDR -corrected cut oFDR -corrected < 0.05.
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We corrected for multiple testing by applying a 0.05 false discovery rate (Benjamini and Hochberg 1995) at the overall model level.
We corrected for multiple testing by applying a 0.05 false discovery rate (Benjamini and Hochberg 1995) to the P values associated with the moderated F statistics that resulted from our contrast matrix.
Significantly differentially expressed genes, highlighted in red in volcano plots (see Additional file 4: Figure S7C), were then sorted by applying a stringent false discovery rate (FDR -corrected cutoFDR -corrected0.001 or less [ 96] and an absolute fold-cutoff threshold of 2.0 or greater.
To identify SDEG, the log2 ratio between uninfected and wild type- or the mutant-infected transcript levels was further screened by applying an unadjusted false discovery rate (FDR) of 5% (q value ≤ 0.05).
Statistical evaluation of enriched Reactome pathways and GO terms for biological processes identified with the innate DB web tool (Lynn et al., 2008) were performed using a hypergeometric test and correcting for multiple testing by applying a Benjamini-Hochberg false discovery rate of 0.01.
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