I have done some Western blots where I have analysed the expression levels of a certain protein in brain homogenates from wild-type and knockout mice. When preparing brain homogenates, I was advised to prepare them in pairs, so that on the same day two brain homogenates, one from a wild-type mouse and the other from a knockout mouse were prepared.
I know that paired analysis is useful for comparing differences visually on the blot between samples from two experimental groups. However, I was wondering whether there are any other benefits (e.g. for statistical analysis) to preparing samples in pairs for a Western blot analysis besides just ease of visual comparison? Any insights are appreciated.