I am handling protein microarray where the lab slides were scanned and data generated using a Genepix 4,000 B scanner coupled to the GenePix Pro & Microarray Acquisition and Analysis Software (Molecular Devices). Once the data is extracted, I subtract the background noise and purification-tag intensities (here is the lab project).
The data from this type of experiments have a mean-variance dependence. I am using VSN package to handle this issue. I am just wondering how the VSN using the
vsn2 function handles the negative intensities and it has an inbuilt log2 as per the explanation on the VSN documentation.