When measuring the relationship between budded and unbudded yeast we do not know if we should include cells with large buds, 75% of the size of the mother cell, as budded or unbudded.
Neither. If you are performing a bud index assay as a proxy for cell cycle distribution you should count unbudded (G1), small budded (S), medium budded (G2) and large budded (M). The problem with bud index assays is one you have alluded to in asking your question: exactly what is the size cutoff for distinguishing S and G2/M phase cells? If you are using this to estimate cell cycle distribution I would actually suggest a fluoresecence microscopy or flow cytometry assay using propidium iodide or DAPI. If you are unable to do that then have a look at Fig S3 in the supplement of our paper "Laulimalide and peloruside A inhibit mitosis of Saccharomyces cerevisiae by preventing microtubule depolymerisation-dependent steps in chromosome separation and nuclear positioning"
James is right. With the budding index you can only reliably distinguish between unbudded G1 cells and all others. It is a good toll to follow cells that come out of a G1 arrest or out of stationary phase. For distinguishing between different cell cycle phases, FACS is best.
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