Installation and Release Notes for Patch to S+ArrayAnalyzer Version 1.1, November 2003
The patch for S+ArrayAnalyzer 1.1 for Windows
fixes several
bugs and provides some enhanced functionality. The patch converts ArrayAnalyzer 1.1 to ArrayAnalyzer
1.1.3. This patch contains all previous patches.
Download
Patch AA11patch3.exe [2.68MB]
After downloading, double-click to run the
patch installer.
These notes are current as of November 2003.
For updates to the installation and other useful
information, please see the support Web site for
ArrayAnalyzer at
http://www.insightful.com/support/ArrayAnalyzer
Contents of these Release Notes
Installation Instructions
This patch to S+ArrayAnalyzer requires that you already have
installed
S+ArrayAnalyzer Version 1.1 Release 1.
To install this patch:
- Close any open S-PLUS sessions
- Click below to download the installer to your Windows
machine.
- Double-click the file to automatically install the patch
and follow the instructions.
Download
Patch AA11patch3.exe [2.68MB]
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 patch 1.1.3; if
you dont require this feature we recommend you use patch
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. A description
of how to use these enhancements is available in the S+ArrayAnalyzer
FAQ.
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. Please
refer to the FAQ
for S+ArrayAnalyzer to see how to specify a design
file for unbalanced experiments.
- 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.
Contact Us
For questions about your S+ArrayAnalyzer license, please
contact a sales representative in your country.
Need help with S+ArrayAnalyzer? See the support
page for information on how to contact a local technical
support engineer.
If you would like to make a suggestion for an enhancement
to S+ArrayAnalyzer or would like to report a bug, please
email bugs@insightful.com.
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