Example data visualization tools within BASE. Images can be resized and exported in several formats. (a) Interactive scatterplot displaying the log2 (ch1 background corrected mean intensity) versus log2 (ch2 corrected mean intensity) pseudocolored according to log2 (ratio). (b) M-A plot  of raw data displaying the intensity-dependent LOWESS  fitted normalization curve in green. (c) Interactive histogram of log2 (ch1 corrected median intensity) viewed in relation to spot flag annotations from image analysis software. (d) 3D Data Viewer displaying a rotatable and scalable MDS  result, in which samples (shown here as spheres) can be visualized in relation to their biomaterial annotations by changing their shape, color, and texture, or by adding floating text.
Saal et al. Genome Biology 2002 3:software0003.1 doi:10.1186/gb-2002-3-8-software0003