Hi everyone, I have 3 samples (Cell) with 3 replicate. In shotgun proteomics 1750 protein with variable expression identified for each sample . How can I found up and down regulation protein between 3 samples? How can I do ANOVA analysis for them? Thanks
Given the N of 3 per group, you're likely to want to share information across proteins. In that case, you could actually just use limma in R/Bioconductor. There happens to be a thread on the Bioconductor list discussing analysing proteomics data here. That thread also discusses possible data transformation methods that you might pursue, since you've not otherwise mentioned anything about the form your data takes.