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In order to validate the results obtained by the differential expressions analysis in our dataset, we perform differential analysis on two independent datasets.
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Both control genes were found to be stably expressed between strains by DESeq2 differential expression analysis (B2m, P=0.286; Gapdh, P=0.972).
Among those groups we performed differential expression analysis between crocidolite-exposed and sham, and detected 5976 differentially expressed genes (p < 0.01, false-discovery-rate (FDR) < 0.022).
Using the WGCNA unsupervised method, they generated modules of co-expressed genes by combining cases and controls instead of gene-wise differential expression analysis.
Differential expression analysis.
Figure 1: Assessment of differential expression analysis.
H.D., E.N.B, performed the differential expression analysis.
Differential expression analysis for sequence count data.
Differential expression analysis was performed using DESeq2 v1.18.178.
Differential expression analysis was implemented using edgeR50 version 3.16.5.
Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.
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