This is a test version of Biostars. For the public version, visit https://www.biostars.org.
how to compare proteomics data?

I have proteome data for control and disease. I should compare their proteins for what differences between them. which tools you recommed? Thank you

proteomics protein blast proteome
• 2,390 views • link
written by siinemselvi • siinemselvi

1 answer

If your data is properly normalized, you can try limma. I have been using limma for LFQ normalized ms/ms data. Of course you need biological replicates (if you have them it is not clear from your post).

• 1 views • link
written by Benn Benn

As per b.nota, limma is quite valid (I have also used it) - just ensure that your data distribution is normal. Others just use standard statistical tests, like t-test, ANOVA, etc. If your data distribution is not normal (or you have low sample n), then ensure that you use a non-parametric test (Mann-Whitney test, Kruskal-Wallis ANOVA, et cetera).

• 1 views • link
written by Kevin Blighe Kevin Blighe

Log in to answer this question.

More posts like this