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Yes, arpen effects turrets. and no, arpen effects jungle creeps too. Also, no, arpen gives you better early game damage, too, because everyone starts with ~20+ armour (or most.. hello fiddlesticks), dropping their armour to 0 gives you better damage early.
AD runes are for laaaaaate game.
And higher crits? Hmm, not really, again, lets say they have.. 25 armour, and neither of you have items. If you have arpen runes, their armour will be reduced to 0, causing you to do MORE damage than if you were to use AD runes, on a crit.
Even on Corki, who can remove up to 110 armour (50 from Gattling Gun, 60 from Black Cleaver), I take armPen runes, because it's so useful early game, and while it won't help if you crush their armour to below zero, it will still help on enemies who stack armour above 110.
I originally bought all of my ArPen runes because I was playing a lot of Garen, and ArPen is great for his early game Judgement damage, which is already high enough as is. Now that I'm playing more Twitch lately and it's equally as nice to get crits of 120+ at level 1 because the enemy effectively has 0 armor.
All this is because LoL, like most games, uses a diminishing returns scale for armor. If 20 armor gives, say, 15% reduce physical damage, 40 armor might only give 25%, instead of 30%, and the gap get bigger and bigger as you stack more armor. For this reason, low amounts of armor at early game give a pretty good reduction in damage, and when you negate all of that armor you end up doing much better damage than you would with AD runes.
End game, AD runes might be better, but honestly endgame runes pages make pretty little difference as 95% of your stats will be coming from your items and level ups anyways. So since early game is really the only time where a rune page can be the deciding factor in a kill or not, I use my rune pages for the best early game combination of runes.
Each 1 of armor you get is like increasing your HP by 1%.
To demonstrate, 100 armor reduces physical damage by 50%. Thus, it takes twice as many physical hits to kill you than if you had 0 armor.
So, by that logic, each 1 point of armor pen is like decreasing the enemy's HP by 1%.
If the gain from the armor penetration runes is bigger than from the attack damage runes, then armor pen is better.
Flat Damage Marks and Quints net you 15 Attack Damage. Per level Damage Marks and Quints net you 36 Attack Damage, with marks matching flats at level 7, and quints matching flats at level 9 Armor Pen Marks and Quints give you 25 Armor Penetration
If you do 100 damage and the enemy has 100 armor, then... Flat damage does 57.5 Per level does 68 at level 18 Armor pen does 57 damage.
50 damage vs 100 armor Flat damage is 32.5 Perl Leve is 43 Armor pen is 28.5
200 dmg v 100 arm Dmg 107.5 Dmg/5 118 ArPen 114
100v200 38 45 36
100 vs 50 79 91 80
SCENARIO: Gangplank (57 vs Dr. Mundo (21 armor) level 1 Damage runes - 59 Armor Pen runes - 57 Parrley Damage runes - 76 Parrrley ArPen runes - 77
It looks like armor pen runes have lost ALOT of their luster, unless my calculations are wrong. The more damage you already have, the better they are, but at middling levels and lower levels of damage, the Damage and armor, the runes are now equal or slightly better.