Additional file 2.

Microarray Quality Metrics Analysis. For a better visualization the microarray data the diagnosis has been split in three groups named 1; Treatment and Time Course. 2; p38α SAPK knock out MEFs and 3; SB203580 treated wildt type MEFs. Section 1 analyses the individual array quality through MA. The mass distribution in an MA plot is expected to be concentrated along the M = 0 axis and there should be no trend in the mean of M as a function of A. A trend in the lower range of A usually indicates that the arrays have different background intensities. A trend in the upper range of A usually indicates saturation of the measurements. Section 2 analyses the array intensity distributions through Box plots and Density plots. Each Box box corresponds to one array. Array duplicates are shown side by side. The left panel corresponds to the red Cy5 channel. The middle panel corresponds to the green Cy3 channel. The right panel shows the Box plots of the log2 Cy5/Cy3 ratio. Box plots are a graphical representation that summarises the distribution of probe intensities across all arrays. It comprises the smallest observation, lower quartile, median, upper quartile and largest observation. All boxes are expected to have similar size and median. Density plots show smoothed histograms of the array signal intensities. The left panel corresponds to the red Cy5 channel. The middle panel corresponds to the green Cy3 channel. The right panel shows the Box plots of the log2 Cy5/Cy3 ratio. The distribution of the arrays is expected to have similar shapes and ranges.

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Ferreiro et al. BMC Genomics 2010 11:144   doi:10.1186/1471-2164-11-144