When you begin Chapter 1 Sector A7 there is a secret room to the left.
There are many energy orbs in a 5 x 5 grid and there is no way around it other than to guess.
Tom comments that "Perhaps we cannot solve this now." This is intended to get you to skip this puzzle until you get to the end of chapter 5 - in the lab you will come across this picture on the table -
Now you know the passcode to the lock. Column 3 Row 2 and Column 5 Row 3. This will open the door and you can enter the room.
You can go back by choosing chapter selecting Chapter Select on the main menu and choosing Chapter 1 section 7.