8 Mouse Samples

DFF is the controls and CKO is the mutant.

basic analysis, see what PCA plots look like and DEGs

coldata
##      treatment sex
## dn15       DFF   F
## dq2        DFF   M
## dz8        CKO   F
## eb3        CKO   M
## fk1        CKO   M
## fk5        CKO   F
## fn3        DFF   F
## fn8        DFF   F

Alignment quality

Pre batch correction: heatmap and PCA

## using ntop=500 top features by variance

Post batch correction: heatmap and PCA

## using ntop=500 top features by variance

Comparisons

1. CKO vs DFF

Differentially expressed genes

Up-regulated Down-regulated Total
CKO vs DFF 86 237 323

Volcano plot

1. CKO vs DFF, padj<0.1, |FC|>1.5