To asses differences between two DNA sequencing methods (454 and MiSeq) I have made artificial mixtures of different bacteria in the lab (mock communities).

An Example might be (numbers are percentages of bacterial cells in the sequenced samples):

• Bacterial strain A: 25%
• Bacterial strain B: 25%
• Bacterial strain C: 25%
• Bacterial strain D: 25%

I have also more complex mixtures (up to 20 different bacteria and other ratios than 1:1, for exp. logarithmic)

If you sequence this you get for example the following results: 454:

• A: 20%
• B: 30%
• C: 24%
• D: 26%

Illumina:

• A: 22%
• B: 28%
• C: 20%
• D: 30%

From every sample (like the one above) I have triplicates.

What statistical test would you suggest to test if there is a significant difference between the two methods (I guess analysing the difference in ratios is the right thing?). Is Chi-Square the right thing if I have three different samples (One is the one mentioned above)? Would even some bootstrapping approach be an idea?

I am familiar with R, so if there is any package you can suggest, that would be nice as well...