Figure 2

Program interface. While running, the program will indicate which genes were found in the dataset, which ones were not present in the array annotation (Annotation.txt file), and which genes are present in the chip annotation but not in the dataset. Progress bars indicate progress for data extraction, refinement, merging, and statistics. Statistics will only be performed when button is activated. In the settings tab on the left, the user can choose between median and mean values to be used for spot selection and ratio calculations. Further, Stouffer’s Z-transform method or Fisher’s method can be chosen to combine p-values from the studies. The user can also chose between automatic Log2 detection, or manual definition. In the latter case “NOLOG” has to be assigned to the folder names of the studies not Log2 transformed.