List of hotfixes for Spotfire S+ArrayAnalyzer

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TIBCO Spotfire S+ArrayAnalyzer 1.1

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AA11patch3: Hotfix for TIBCO Spotfire S+ArrayAnalyzer 1.1 (Released: November 01, 2003)

The hotfix for S+ArrayAnalyzer 1.1 for Windows fixes several

bugs and provides some enhanced functionality. The hotfix converts ArrayAnalyzer 1.1 to ArrayAnalyzer 1.1.3. This hotfix contains all previous hotfixes.

See Release Notes for more details (Note: for this link to work, you must be logged in to the TIBCO Support Portal)  

Installation Instructions

This hotfix to S+ArrayAnalyzer requires that you already have installed

S+ArrayAnalyzer Version 1.1 Release 1.

To install this hotfix:

• Close any open S-PLUS sessions
• Download the hotfix installer to your Windows machine.
• Double-click the file to automatically install the hotfix and follow the instructions. 

Fixed Bugs

ArrayAnalyzer 1.1.2

• Reading cDNA data from the Import cDNA Data dialog may have resulted in

   

  incorrect values if there are missing columns (denoted by two or more tabs) in

   

  the data file. The data will now be read correctly even with missing column

   

  values.

• The RMA composite procedure from the Affymetrix Expression Summary took

   

  the log (base 2) twice.

• When reading Affymetrix MAS 5 data from the Import Affymetrix Data

   

  dialog, the threshold for taking the log (base 2) of MAS 5 data was 1,

   

  it is now 0.1; i.e., if the log transform is requested (the

   

  default), the expression data returned for MAS 5 data is

  log2(ifelse(data < 0.1, 1, data))

  The threshold for MAS 4 data is still 1.0

Enhancements

ArrayAnalyzer 1.1.3: On Windows, added ability to read in Affymetrix CHP files and 

ability to read in Affymetrix Version 4 CEL files (binary version). This is the only change in hotfix 1.1.3; if you dont require this feature we recommend you use hotfix 1.1.2.

ArrayAnalyzer 1.1.2:The dialogs and functions have been modified to allow the reading of experiments with more than two levels in Affymetrix arrays. 

These enhancements also allow the reading and analysis of data from unbalanced experiments; now, the number of replicates within each level does not have to be the same for all levels. These changes include the following updates to the GUI:

• Adding a field for the number of levels in the Import Affymetrix Data dialog. For example, if you had a three level experiment with four arrays for treatment level 1, and three arrays for treatment levels 2 and 3, you would set the Levels to 3 and Max. Replicates to 4. Note that the Replicates field in this dialog is now labeled Max. Replicates. 
• The MVA pairs plots created by the Normalization and Expression Summary dialogs now handle more than two levels.
• The Differential Expression Analysis dialogs (Local Pooled Error Test and Multiple Comparison Test) each have two new fields, Compare Level 1 and Compare Level 2, where you can specify which two levels are to be tested.

The list of chips in the Chip Name field on the Import Affymetrix Data dialog has been extended to include the new Affymetrix chips: moe430a, moe430b, rae230a, rae230b.