Hello,
I have 11 proteins in two datasets: with 5 in 1st and 6 in 2nd dataset. I have calculated the amino acid percentage for three amino acids (A, R, N) in them as shown in the attached file from excel 
I want to normalize them by background amino acid probability of all proteins in two datasets and then conclude, for e.g., basic amino acids (R) are enriched or hydrophobic amino acids (A) enriched. Kindly help.
Thank you!
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bioinfo8
1 answer
Percentages and frequencies are already a form of normalization, aren't they?
May be what you mean is how to test whether proportions of certain types of aa are significantly different in the two sets . A Fisher's exact test will do the job.
Papers related to what? Fisher's exact test?
I am not aware of references doing this kind of analyses, sorry. But running a Fisher's exact test to compare proportions of amino acids is straight forward. Yes, do it in R.
I will suggest to start with some basic R tutorial, there are lots in internet. Once you are familiar, prepare a matrix of 2x2 for your proportions and run the Fisher test.
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