Welcome to Countermeasures!
I have used the warframe wiki to find damage output information for my Tenno to use against enemies of all faction types. There came a point that I wanted to know what types of damage my enemies were dealing to my Tenno, as a faction, and as higher class enemies. I noticed very quickly that I needed to jump between multiple pages to find information on just one faction, from physical to elemental damage, to the rules governing alarm triggered enemies (Prosecutor, Bursa, Juggernaut Sentient) damage and armor types. So I poured over those pages (Damage (and all subcategories for physical and elemental types), Factions (each individual Grineer, Corpus, Infested, and Corrupted enemy page) and gathered the necessary information to make a framework (March 30, 2017 ish), and have come back to try to iron out some of the wording and just double-check to make sure there isn't anything I could possibly add at this point of my understanding and re-emerging HTML skills (April 1, 2017).
Please, remember to use your critical thinking skills while referencing this information. Higher level players who utilize power-heavy builds may not need any of this information, vis-a-vis Newer and/or Niche players may utilize it more.
This page is for players who want a quick-reference for a targeted boost to their defenses versus specfic enemy types (faction, mission type, alert level).
Incoming Damage Process (Basics)
Shields will deplete, then Armor mitigates the damage to your Health. As the base, general framework for all incoming damage to your Tenno. You will have to consider specific factors when researching different enemy and map types.
Impact > Shields > Puncture > Armor > Slash > Flesh
This line represents incoming damage, and how it works through your defenses to get to your squishy Warframe flesh. If you point to any factor above, the preceding factor receives some type of advantage against it. Also, for example, Puncture damage must first pass through Shields, then Armor, to hit Flesh.
The circular...umm...diagram? maybe? That thing above shows the circular nature of physical damage and damage mitigation. This is the down and dirty "checks and balances" of Physical damage.
If you pick any factor, then draw a line "straight across" from it (i.e. Shields to Slash or Armor to Impact), you will find the damage type or mitigating factor that receives neither a bonus nor a weakness when interacting with your chosen starting factor.
Physical Damages Vs. Mitigating Factors
Grineer and Corrupted fodder enemies deal Impact damage.
Corpus enemies don't deal Cold damage specifically, but their Eximus units sometimes have Cold shields.
Infested Ancients sometimes use Magnetic damage.
Corpus and Corrupted fodder enemies deal Puncture
Toxin damage is always present, in some form, when dealing with the Infested.
Infested Ancients sometimes use Corrosive damage.
The Infested use Slash damage the most, the Grineer and Corpus use it a little less, and the Corrupted use it the least.
Shields are effective against Puncture and Radiation , and just a good thing to have. Mostly used when fighting Corpus and Corrupted . Its useful to have a rechargeable buffer, unless your in a situation where your enemy is dealing Toxin damage.
Armor is effective against Slash and Blast , and just a good thing to have. Useful with all enemies to varying degress. Most useful against the Infested and Grineer , the Corpus deal it to a nominal extent, and the Corrupted deal it to a lesser extent. It is useful to have a high damage mitigation, unless you are in a situation where your enemy is using Puncture, Toxin, or Corrosive damage.
Flesh is one of your Health classes as a Warframe. It holds your circuits in, and moves your tiny Oberron arms. Those things are necessary to achieving greatness. Not so much if you favor crawling your way to victory during bleedout.
Enemy Physical Damage and Elemental Considerations
In certain situations you may want to consider elemental resistances for your Warframe. More useful for endless objective missions where you farm for 45 minutes while the random tries to extract after 10. Silly randoms, we're here to farm bro!!
The majority of Grineer utilize Impact damage
The Grineer faction list shows they have enemy types that deal Heat and Electricity.
Heat damage is only weak against Proto-Shields, which you do not have normally.
Electricity damage is weak against Alloy armor, which you do not have normally.
You may want to equip Resistance Mods when facing the Grineer.
The majority of Corpus utilize Puncture damage.
The Corpus faction list shows they have enemy types that deal Electricity, Heat, Radiation, and Blast.
Electricity and Heat are mention above, in the Grineer section.
Radiation damage is weak against Shields, so you may want to buff your Shields.
Blast damage is weak against Armor, so you may want to buff your Armor.
The majority of Infested enemies deal Slash damage
The Infested faction list shows they have enemy types that deal Electricity, Toxin, and Magnetic.
Electricity was covered earlier, in the Grineer section.
Toxin bypasses Shields AND is effective against Flesh. So you may want to buff your Armor as well as equipping a Resistance Mod.
Magnetic damage is weak against Alloy, which you do not normally have, and it is effective against Shields. You may want to buff your Armor as well as equipping a Resistance Mod.
The Corrupted deal a healthy mixture of Impact, Puncture, and Slash.
The Corrupted faction list shows they have enemy types that deal Electricity, Heat, and Blast. All of these were covered above.