Difference between B-Phycoerythrin and R-Phycoerythrin

No difference. R and B are just the labels that refer to the type of algae they are derived from :)

B-Phycoerythrin (B-PE), a fluorescent protein from phycobiliprotein family, is isolated from cyanobacteria and eukaryotic algae. Its primary absorption peak is at 545nm with a secondary peak at 563nm. B-PE consists of α, β and γ subunits and is present as (αβ)6γ. B-PE and the closely related R-PE are the most intensely fluorescent phycobiliproteins having orange fluorescence. They are significantly brighter and more photostable than conventional organic fluorophores. B-PE labeled streptavidin, primary and secondary antibodies have been widely used in applications such as flow cytometry and multi-color immunofluorescent staining.

While

R-phycoerythrin (R-PE) is an intensely bright phycobiliprotein isolated from red algae that exhibits extremely bright red-orange fluorescence with high quantum yields. It is excited by laser lines from 488 to 561 nm, with absorbance maxima at 496, 546, and 565 nm and a fluorescence emission peak at 578 nm. R-PE is a large molecule used for fluorescence-based detection, primarily in flow cytometry, microarray assays, ELISAs, and other applications that require high sensitivity but not photostability.