I have 51 unmatched samples and 22 matched SNParray data. I only want to use the logR values for my downstream analysis and I have the probe intensities for each samples. For the matched ones I am calculating the logRs this way: log2(tumour probe intensity/normal probe intensity).
However, for the 51 unmatched samples I want to pool the 22 normal samples to then calculate the logR values. In order to make this panel of normals, would it be best to mean the probe intensity of each probe in all of normals and then do log2(tumour probe intensity/panel of normal probe intensity)?