Just extract the total lipid using folch method . Then go on to make the methyl esters and subject it to gas chromatography. You will get the relative amount of each different fatty acid in your sample.Then its simple to calculate the ratio of n3/n6.
Mayo Medical Labs does a test called comprehensive fatty acid profile (CFA). The specifics of the test can be found at http://bit.ly/1AtZ7. I have used Mayo Medical Labs for well over 15 years & can calculate many different ratios from the specific testing done in this panel. This includes w-6/w-3, LA/DHA, AA/EPA along with many other individual tests. This is not a cheap test & costs about $300.
I doubt if the ratio of all omega 6 to all omega three is very useful. The ratio of linoleic acid to alpha linolenic acid is of value, since these compete for processing by delta 6 desaturase, and should be consumed in a balanced way. Again the ratio of arachidonic acid to eicosapentaenoic acid is important as too high a ratio could promote inflammation.
The w-6/w-3 is very well established in the peer-reviewed literature as is the AA/EPA ratio. Both are indicators of inflammation if elevated. Sears says optimal ratio is about 1.5. LA/DHA ratio is also helpful if patients can keep < 10. In all of these ratios the key omega-6 fatty acids are linoleic acid (LA) & arachidonic acid (AA). The key omega-3 fatty acids are EPA and DHA. The Mayo Medical Labs comprehensive fatty acid profile (CFA) quantitates many of the fatty acids which can provide additional clues to the healthcare practitioner re:
1. Is the patient eating foods high in AA: (e.g., animal meat, egg yolk)
2. Is the patient eating out a lot or eating too much processed foods or too high a consumption of nuts containing LA. High normal or elevated LA indicates any or all of the above.
3. Is the patient's supplement of omega-3 fatty acids sufficient vis-à-vis levels of EPA and DHA which should be at least [2]x upper limit of "normal" per the CFA report. I recommend Eicosamax liquid which contains EPA 1500mg, DHA 1200mg per tsp (5cc). Titrate the dose per the Biological End Point (BEP) as seen using the CFA report. I have used this approach for about 15 years in my patients & it correlates well with dietary history. Just wish the Mayo Medical Labs were less expensive.