• Practicalities of our Experimental Design

• Different 10X runs at different times OR just the same sample run twice

• Obscure real biological changes

A few ways our data can be arranged (software dependent too)

• single sample SCE objects QCed in isolation

• large SCE object containing many samples

• multiple large SCE objects with multiple samples

Important we make sure things match up

• Different bioconductor versions

• Different analysts may have formatted things differently

A useful quick look