Differential expression runs with DESeq2. Link to code.
I think what ended up being the most interesting is the combined run accouning for sex and treatment, All of the observed differences in expression appear to be sex-based, but this in and of itself is interesting and it gives us the IDs of 2370 differentially expressed lncRNAs between female and male sample groups.
Combined Run
Volcano Plot
- 2370 significantly differentially expressed lncRNA
PCA - treatment
PCA - sex
PCA - treatment - labelled
PCA - sex - labelled
Top 50 Heatmap
- Clustered by sex
Female Run
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- 1 significantly differentially expressed lncRNA
PCA - treatment
PCA - treatment - labelled
Top 50 Heatmap
- Clustered by treatment group
Male Run
Volcano Plot
- 5 significantly differentially expressed lncRNAs
PCA - treatment
PCA - treatment - labelled
Top 50 Heatmap
- Clustered by treatment group