I'm trying to get straight in my head the difference between GetBaseAV and GetPermAv for the Player. The Wiki page for GetBaseAV refers you to the stat page and you find that base values are ones assigned in the Geck. That's fine. What it doesn't tell you is that the base values also appear to be modified by the level-up menu and by the tag skill bonuses - this may already
be obvious to everybody except me

GetPermAV has added to my confusion because the Wiki page http://geck.gamesas.com/index.php/GetPermanentActorValue says this function "Returns the permanent value, no bonus from perks, equiped items ect." - And this doesn't seem to be the case as far as Perks are concerned. They appear to be included.

I went through the trouble of writing down all the player starting stats during the goat, and tracked a couple of stats through a few levels:

Small Guns up to level 4:
1. Goat started with 19, tagged it for 15 bonus to 34
2. Added 5 points during a level up
3. Added two 'Gun nut' perks +5 each
4. Wearing armor with +5 small guns

So after these steps, the Pipboy shows 'small guns' at 54 +
At the console,
Player.GetAV returns 54
Player.GetPermAv returns 49 - seems to include the Gun nut perks but not the armor
Player.GetBaseAV returns 39 - includes Goat 19+15, and the level-up +5

Medicine:
1. Goat started with 15
2. Took the Bobble +10

Pipboy shows 'Medicine' 25
Player.GetAv returns 25
Player.GetPermAV returns 25 - includes the bobble
Player.GetBaseAV returns 15

Barter:
1. Goat started with 15
2. FOOK threw in the 'Scoundrel' perk after the goat +5
3. Read one Barter skill book +1
4. Wearing Armor item for +2 Barter

Pipboy shows 'Barter' 23 +
Player.GetAv returns 23
Player.GetPermAV returns 21 - includes the Perk and Book, but not the armor.
Player.GetBaseAV returns 15

So the results i'm getting for GetPermAV would make sense to include bobbles, books, and perks - for the perks that are never removed.

Am I missing something?

Hmm. I'm wondering what would happen with Impartial Mediation, which adds 30 points to Speech but only when your Karma is Neutral.

I think the part about 'no bonus from perks' is only partially true, and certainly misleading. I've always gone by the assumption that the permanent value is the base geck value + any modifications to that that aren't supposed to be removed during the course of normal gameplay. Certain perks, all spells, and all wearable armor effects are temporary in nature and are excluded when totaling up the perm value, so that line in the wiki description can't be taken completely literally.

Whether a modifier value contributes to the perm value or not I think depends on which type of modifier is used to offset that value. Game and script modifiers appear to affect the perm value, while the magic modifier doesn't seem to... and it seems to me that all the things mentioned that don't change the perm value (armor, certain perks, etc..) all use enchantments of some sort, which would be a magic modifier.
"Base value + all modifiers = GetAV value" can be broken up into "Base value + perm modifier = GetPermAV value" & "GetPermAV value + temp modifier = GetAv value"..
or (base+perm)+temp=GetAV.

That makes sense. Thanks for clarifying it!