Read count normalization
First, we removed reads mapping to 7 genes encoding ribosomal RNA
subunits and hemoglobin genes to remove the influence of blood
contamination on the skin biopsies. While investigating RNA integrity,
we removed two samples with low RNA quality (retaining samples with RQN
> mean - 2 standard deviations), leaving a final sample
size of 36 geladas (n =20 males, n =16 females). We then
removed genes with low expression (median TPM < 10) for either
males or females and 14 Y-chromosome genes (removing sex differences
that are a product of their location on the male-specific Y-chromosome),
which resulted in 10,212 detectably expressed genes for our downstream
analysis. We normalized read counts using the voom function in
the R package limma(Ritchie et al., 2015).