I am trying to use Limma to analyze differential expression in processed, log2 transformed proteomics data. I have been following this code: http://www.biostat.jhsph.edu/~kkammers/software/CVproteomics/R_guide.html
However, for some of the analysis the p-values look very strange and the volcano plots show no spread, they are all in a line.
Looking deeper into the analysis outputs it seems as it is apparent something is going wrong with eBayes step. s2.post (posterior value of variance) is the exact same as s2.0 (estimated prior value of variance) and does not differ between gene. and the df.0 (degrees of freedom for s2.0 ) is inf
Any insight into what might be going wrong or how I can trouble shoot would be appreciated!