percentage of amino acids, normalize by background amino acid probability
1
1
Entering edit mode
5.6 years ago
bioinfo8 ▴ 180

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 enter image description here

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!

Amino acid percentage normalization excel • 2.0k views
ADD COMMENT
2
Entering edit mode
5.6 years ago
abascalfederico ★ 1.2k

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.

ADD COMMENT
0
Entering edit mode

Hello, thank you for the answer. Can you please guide me further and refer some related papers. Thank you.

ADD REPLY
1
Entering edit mode

Papers related to what? Fisher's exact test?

ADD REPLY
0
Entering edit mode

This kind of analysis using the test, thanks. I think I can do with R.

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

Ok, I will try to find out some papers and consult you for further analysis.

ADD REPLY
0
Entering edit mode

These are few papers: 1) Paper 1 2) Paper 2 Now I am stuck on how to arrange data so that R can read it, then I can use fisher.test function and wish to get output in the mentioned papers. Kindly guide. Thanks.

ADD REPLY
1
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2645 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6