probeNames returns a string with the probeset names for each probe on the array.

probesetNames, on the other hand, returns the unique probeset names.

I couldn't really understand the difference from the definition.

I tried to run the functions on the raw_data file. probeNames(raw_data) returned a vector with ~33000 unique PROBEIDs (I ran the table() function on the output), equal to the number of entries I got after running the rma function on the data with target = "core" (gene level summarization).

I also tried running probesetNames(raw_data) and I got a vector with ~257000 unique PROBEIDs, equal to the number of rows from running rma with target = "probeset" (exon level summarization).

Given that, I still cannot really understand the difference.

Note that I'm working with Affymetrix GeneChip Human Gene 1.0 ST Array