Entering edit mode
I have a question on limma differential testing on proteins.
I have the script that can reproduce the plot in the link. My question is why Limma would generate the volcano plot as described, as I failed to see anything suspicious in my data set.
Thanks for your response. Is this a problem in statistical inference? Is there anything I should do to minimize the effects?
Whether or not this is symptomatic of a problem depends on what the data is, which is something you don't give much information about.
If this is real proteomic data from biological replicates, then this phenomenon is not a good sign. It can often arise from a strong batch effect that hasn't been accounted for.
If you want to discuss this, then please post a new question with some relevant background about your experiment. But first explore your data by making some plots (plotMDS, plotMD, plotSA etc).