In addition, make sure to change the Exclude fusion if minimal size < from 5 to 0kb to ensure that you get read-through fusion genes.

For single end fusion detection where you have paired reads, it makes sense to first align to the genome (but choose the option to export unmapped reads).  Then, use this file for the single end fusion detection module.  This ensures that you are using unmapped, unpaired reads as the input for fusion. 

This is caused by a known Microsoft .NET bug, and can be fixed by going to : http://www.omicsoft.com/software/FixDefaultProxySettings2009.exe 

Make sure to save this file to your desktop, run it, then restart your computer to resolve the issue.

PLATFORM VERSION INFO
      Windows                   : 5.1.2600.131072 (Win32NT)
      Common Language Runtime         : 2.0.50727.42
      System.Deployment.dll               : 2.0.50727.42 (RTM.050727-4200)
      mscorwks.dll                 : 2.0.50727.42 (RTM.050727-4200)
      dfdll.dll                   : 2.0.50727.42 (RTM.050727-4200)
      dfshim.dll                 : 2.0.50727.42 (RTM.050727-4200)

SOURCES
      Deployment url                 : http://www.omicsoft.com/software/ArrayStudio30/ArrayStudio.application

ERROR SUMMARY
      Below is a summary of the errors, details of these errors are listed later in the log.
      * Activation of http://www.omicsoft.com/software/ArrayStudio30/ArrayStudio.application resulted in exception. Following failure messages were detected:
      + Downloading http://www.omicsoft.com/software/ArrayStudio30/ArrayStudio.application did not succeed.
      + The remote server returned an error: (407) Proxy Authentication Required.

COMPONENT STORE TRANSACTION FAILURE SUMMARY
      No transaction error was detected.

WARNINGS
      There were no warnings during this operation.

OPERATION PROGRESS STATUS
      * [28-Apr-09 11:16:08 AM] : Activation of http://www.omicsoft.com/software/ArrayStudio30/ArrayStudio.application has started.

ERROR DETAILS
      Following errors were detected during this operation.
      * [28-Apr-09 11:16:13 AM] System.Deployment.Application.DeploymentDownloadException (Unknown subtype)
      - Downloading http://www.omicsoft.com/software/ArrayStudio30/ArrayStudio.application did not succeed.
      - Source: System.Deployment
      - Stack trace:
      at System.Deployment.Application.SystemNetDownloader.DownloadSingleFile(DownloadQueueItem next)
      at System.Deployment.Application.SystemNetDownloader.DownloadAllFiles()
      at System.Deployment.Application.FileDownloader.Download(SubscriptionState subState)
      at System.Deployment.Application.DownloadManager.DownloadManifestAsRawFile(Uri& sourceUri, String targetPath, IDownloadNotification notification, DownloadOptions options, ServerInformation& serverInformation)
      at System.Deployment.Application.DownloadManager.DownloadDeploymentManifestDirectBypass(SubscriptionStore subStore, Uri& sourceUri, TempFile& tempFile, SubscriptionState& subState, IDownloadNotification notification, DownloadOptions options, ServerInformation& serverInformation)
      at System.Deployment.Application.DownloadManager.DownloadDeploymentManifestBypass(SubscriptionStore subStore, Uri& sourceUri, TempFile& tempFile, SubscriptionState& subState, IDownloadNotification notification, DownloadOptions options)
      at System.Deployment.Application.ApplicationActivator.PerformDeploymentActivation(Uri activationUri, Boolean isShortcut)
      at System.Deployment.Application.ApplicationActivator.ActivateDeploymentWorker(Object state)
      --- Inner Exception ---
      System.Net.WebException
      - The remote server returned an error: (407) Proxy Authentication Required.
      - Source: System
      - Stack trace:
      at System.Net.HttpWebRequest.GetResponse()
      at System.Deployment.Application.SystemNetDownloader.DownloadSingleFile(DownloadQueueItem next)

COMPONENT STORE TRANSACTION DETAILS
      No transaction information is available.

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.