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
