Our ability to detect expression of genes by qPCR, most at levels well above background, in 3' amplified samples led us to hypothesize that buccal samples could be used for differential expression testing by microarray analysis.
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.
Differential expression testing was performed by generalized linear modeling of indicated (co- variates on normalized log2-transformed expression values implemented by limma Bioco- variatesckage (Smith, 2005).
Overall, differential expression testing resulted in a reduction of the number of candidates by ~60-70 ~60-70ing ~300-500 genes per donor region that need further testing.
Differential Expression Testing For the 40 subjects, we compared cases and controls stratified by race/ethnicity.
We also compared naiveLu, a simple method for identifying differentially expressed genes by simply applying a differential expression test directly without accounting for sample heterogeneity.
This framework contains new normalization methods based on generalized Poisson distribution modeling sequence count data, followed by permutation-based differential expression tests.
In the following sections, we use an analysis of the PCA loadings (Supplementary data S 2 S 5) together with specific pairwise differential expression tests by DESeq (Supplementary data S 6 S 28) to fully characterise the significant changes in gene transcription in the different lysozyme induction experiments, with particular focus on the T+3 transition states in the T70N and I56T variants.
For the comparison between tissues, we treated the three time points sampled as biological replicates, estimated transcript-wise dispersion values, followed by differential expression analysis with edgeR's exact test [ 117].
For each lncRNA, its knockdown expression data were used to determine the affected genes by differential expression analysis (fold change > 2 and t-test with FDR < 0.05).
