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Expression Console
v1.1 Launches
Expression Console v1.1 is now
available.
Expression Console is freely available software from Affymetrix
which performs signal estimation on 3' expression, gene-level and
exon-level expression arrays and enables quality control determinations. Detailed release notes are available which document the latest
changes. Download the 40 MB installer directly.
Integrated Genome
Browser Updated (now at v4.56)
Affymetrix’ open source genome browser IGB has been recently updated, including an updated UserGuide. View the Release Notes for details on the latest and greatest improvements. Questions on IGB? Visit the IGB Discussion Board.
CNAT 4.0.1 Now
Available
CNAT
4.01 User Interface, CNAT
4.01 Copy Number Pipeline and updated CNAT
Support Materials are now available for download.
CNAT 4.0.1 addresses the following four issues identified in CNAT
4.0:
- LOH
algorithm results corrected: LOH.CNT files are now correct in both the
user interface and command line tools.
- Virtual
set CHP file order issue has been addressed in the user interface
tool.
- File
name character limit in CNT header has been addressed in the user
interface tool.
- Update
to HMM LOH State metric to improve LOH data interpretation
- LOH
State of 1 now indicates LOH while an LOH State of 0 indicates
retention in both the user interface and command line tools.
- LOH
and Retention probabilities have also been combined into a single
graph for a more intuitive display in the user interface
tool
IMPORTANT
NOTE: If you have run LOH analysis and created
LOH CNT files, re-analyze these samples using CNAT 4.0.1 to create updated
files.
More File Format Documentation
New documentation is available for the following file formats: PGF, CLF, & BPG
Human Gene ST1.0 Released
Affymetrix recently launched the new Human Gene ST 1.0 Array for gene-level expression analysis. Tissue panel sample data are all available as GCOS CEL files. AGCC formatted ARR/CEL/CHP files will be available shortly. A complete list of other necessary supporting documentation can be found on the Human Gene ST 1.0 Support Page.
Tissue Panel Mixture Data Set on Human Exon, Gene, and U133
Available from the Human Gene ST 1.0 Sample Data Page, Affymetrix has released a set of tissue mixture data run on the Human Exon 1.0 ST Array, Human Gene 1.0 ST Array, and the Human U133 Plus 2.0 Array. These data are available as GCOS CEL files. AGCC formatted ARR/CEL/CHP files will be available shortly.
AGCC Formatted Sample Data for Tiling Product Line
Sample data for nine different formats of tiling arrays are now available. Data are available as GCOS CEL/BAR files for all and two array types have AGCC ARR/CEL formats.
Support Files Now Available for SNP 5.0
We have recently released all available support and analysis files necessary for analysis of the new SNP 5.0 array.
Changes in NetAffx Annotation Flat Files
Look for some changes coming in our NetAffx annotation file formats. 1) We?ll be adding commented headers to our CSV files. 2) We have decided to discontinue the four 'protein family' annotations (SCOP, EC, P450 and hanks kinase). Note that this change may affect third-party parsers.
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