I am very new to proteomics data analysis. I have a proteomics data set which looks like the below example:
Proteins a b c d Protein 1 57038.57 75498.98 223940.89 47389.90 Protein 2 92730.64 NA 83930.36 434893.34 Protein 3 NA 84930.45 783.37 8903.23 Protein 4 83929.36 NA NA 74830.03
I am not sure how to proceed with the normalization process because of the "NA" values. I tried to get some information regarding this and in some cites it is mentioned to change NA to "0" or to assign values like 0.0001 to NA. Could someone please guide me which is best method to do the normalization and which R package would you prefer for the same?
Many thanks in advance