The following preprocessing operations can be performed using BW-DEGS
1) Background Correction Method (Preprocessing >> Background Correction Method): A first preprocessing step is the Background Correction. The idea behind the Background Correction is that the fluorescence of the spot is the effect of summation between the fluorescence of the Background and the fluorescence due to labeled mRNA .Thus the theory goes, in order to obtain the values proportional to the amount of mRNA, one needs to subtract the values corresponding to the Background. In this context we used the RMA and MAS methods.
2) Normalization method (Preprocessing >> Normalization method): The goal of this step is to align the distribution of the probe intensities in a set of array. In other words, after this normalization all arrays should have the same distribution of their probe intensities. This can be done in several ways; the most used is the quantile normalization.
3) Summary Method (Preprocessing >> Summary Method): After normalization, one may want to do a probe specific correction, and a summarization to probe set level data on log scale. Various methods are available in this case.
4) PM Correction Method (Preprocessing >> PM correction Method): This step including a MM probe is to provide the value that estimate the background nonspecific hybridization as well as any other stray signals affecting the PM probe.
After preprocessing, a window is displayed that allows the registration of the gene expression matrix.
After recording the results, two windows appear.
