I have three different proteomics data sets, each of them in duplicates. Regardless of the problem not having triplicates for statistical power. I wpuld like to know in general how I can analyse the differential expression (quantitative analysis) of the two conditions in each of the runs.
One of the experiments is SILAC, the other two are label-free. I would like for each run to compare the two condition to check for statistically significant changes.
My idea was something bases on the (pair-wise) analysis of microarrays, but I am not sure exactly (if at all needed) how to normalize the data sets.
The data I have is the output from the maxQuant (excel sheets with loads of columns, in some of them it says Ratio H/L normalized). Does it means I don't need to normalize the data again?
thanks for any help Assa