Array Studio offers a number of different modules for quality control and microarray data. In the Microarray menu, under QC, Array Studio offers Correlation-based QC, Model-based Outlier Detection, Principal Component Analysis, and the QC Wizard.

In addition, under the Summarize menu, Array Studio offers Kernel Density and Pairwise Correlation modules.

Finally, for Affymetrix data, a MAS5 QC Report can be created, by going to the Microarray Menu | Affymetrix | Generate Affymetrix MAS5 Report (3'IVT Arrays). This generates a classic Affymetrix QC Report, including the options to generate 3' to 5' ratios for selected control genes (as well as the standard Background, Scaling Factor, RawQ, etc.).

The QC Wizard allows the user to run Correlation-based QC, Model-based Outlier Detection, Principal Component Analysis, Pairwise Correlation, an the Kernel Density modules all together (but offers less individual options).

Correlation-based QC is a statistical module that looks for outliers on a per-group basis.

Model-based Outlier Detection performs outlier detection on a per-variable basis, and creates a new dataset, with these outliers removed.

Principal Component Analysis can be used to look for structure in the data, as well as detect outliers.

Kernel Density is a classical QC method for microarray data, and shows the density of each chip, by intensity.  It can be used to look for outliers.

Pairwise correlation will calculate pairwise correlation values for observations, and a correlation matrix will be generated (along with some correlation views).  This is useful in detecting outliers per-group, as well as outliers to the dataset as a whole.