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.

Dear Keniajin,

please check the article Variance stabilization applied to microarray data calibration and to the quantification of differential expression DOI: 10.1093/bioinformatics/18.suppl_1.s96

PDF at https://www-huber.embl.de/pub/pdf/huber_ismb2002.pdf

Hope this helps,

Wolfgang