4.3 Integration

Integration analyses are done in this section following designs specified by El Chérif. Analyses were first done using the closest human ortholog (Section 4.3.1). For microarrays, mapping from probes or probesets to genes were done using the original author annotations, completed with available R Org.db modules.

Analyses were then repeated using the original Gene name for rat or mouse (Section 4.3.2). For microarrays, mapping from probes or probesets to genes were done using Biomart latest annotations, or using megablast queries when unavailable (GSE42940). Probes with mapping to multiple genes are discarded.

For RNA-Seq, log2FoldChange use in this integration section is the Normal shrinkage and not the Apeglm that was considered too stringent for this kind of analysis.