seeking advice on setting up a database

I have previously managed to organize information about rock thin sections in a spreadsheet, but one winds up with lots of extra columns needed to keep track of everything, and lots of empty cells since not every mineral appears in every rock, and not all possible information about each mineral is recorded for every sample. Therefore I have been thinking of creating a database to keep track of it, but am running into issues with the design phase.

I have found pages on line that describe how to "normalize" your data to make certain you aren't wasting storage space on redundant data. One of them had an example where they started with one table that contains a list of student numbers, the name of each student's advisors, the room number of the advisor, and all of the classes each student takes. They then point out that it is better to break this into separate tables, and after a few steps they wound up with one table for showing which students have which advisor, one table showing which advisor has which room, and one which shows which students take what classes.

I can follow this logic, and if I had so few levels of information I would already be done creating my database. However, geology is more complicated than that.

( a summary of what all I have that I want to beat into a database. Please read if you can give me any advice as how best to group this stuff into appropriate tables )

I suspect that to those of you who are used to working with databases this will seem like a very simple, straightforward, easy to solve problem. If so, please tell me how to approach this! How many tables to I need to create? How do I best link them?