This module of Babelomics is intended for the visualization of raw data. It is a tool complementary to the Normalization module of Babelomics. Both tools work over the same raw data and have a similar input requirements.

Select the Affymetrix or the TwoColors button in the form in order to indicate which platform you are analyzing. If you are normalizing a two color platform then you also need to indicate the Array type you are using. Selected plots will be displayed in png format.

• Box-plot: displays Box-plots for each of the arrays in your raw data. Just perfect match probes are used.

• PM and MM distributions: displays histograms of the perfect match and mis-match probes for each of the arrays in your raw data.

• RNA digestion: a line is displayed for each array aiming to detect possible RNA degradation. Within each probe-set, probes are numbered directionally from the 5' end to the 3' end. Within each array, probe intensities are averaged by probe number, across all genes in the array. These means are represented with a line for each chip.

• MA plot: displays MA-plots of each of the arrays against a pseudo-median reference computed across all arrays in the raw data.

• Raw image: represents the raw data mimicking scanner image.

• Box-plot: Log-ratios of the red -Cy5- foreground channel over the green -Cy3- foreground channel (i.e. M-values) are displayed in a Box-plot for each array.

• MA plot: displays MA-plots of each of the arrays.

• Density: displays density plots of each of the foreground channels in the microarray.

• Printip: print-tip loess curves are displayed over an MA-plot for each of the print-tip blocks in the array. Cannot be applied to microarray platforms which do not have a print-tip structure like Agilent for instance.

• Foreground vs. Background plot: displays foreground versus background intensities for each array.