The bioBakery help forum

Adjust_batch_diagnostic file

Hi there,

I followed the CRC tutorial and I was wondering if you could explain what the adjust_batch_diagnostic.pdf file is showing us, after running the adjust_batch function in MMUPHin ?

Thank you,

It’s essentially comparing the feature mean parameters and mean abundances before and after adjustment.

On the left, Gamma is a parameter characterizing the mean of each feature by batch. If the adjustment had done nothing, the points would all fall on the y=x line. Instead, they’re shrunken toward 0, meaning the batch parameters have become more similar.

On the right, it’s comparing the mean of each feature by batch before and after adjustment. Each black/red pair of connected dots is a feature, and each dot is that feature in a particular batch. The red dots are slightly shifted to the right to prevent overlapping their black counterparts.

@sma might have more to say on this if I glossed over / mischaracterized any important details.