ChipInspector Release Notes

September 2011: ChipInspector Release 2.1

Data updates:

Probe annotation is based on ElDorado 08-2011.
The following new chip is supported:
- X_tropicalis Genome (Xenopus tropicalis, western clawed frog)

December 2010: ChipInspector Release 2.1

Data updates:

Probe annotation is based on ElDorado 12-2010.

February 2010: ChipInspector Release 2.1

Data updates:

Probe annotation is based on ElDorado 02-2010.
The following new chips are supported:
- Affymetrix Poplar Genome
- Affymetrix Vitis vinifera (Grape) Genome
- Affymetrix Human Gene 1.1 ST Plate

July 2009: ChipInspector Release 2.1

Data updates:

Probe annotation is based on ElDorado 07-2009.
The following new chips are supported:
- Affymetrix Human Genome Array Plate
- Affymetrix Mouse Genome Array Plate
- Affymetrix Rat Genome Array Plate
- Illumina Human HT 12.0 Version 3

September 2008: ChipInspector Release 2.1

Update of the underlying Netbeans platform to resolve proxy issues.
Combination of data files for statistical analysis was improved. Previously possible combinations could be ignored if treatment and control lists were not of the same length for exhaustive and random pairing.
Header of exported probe/transcripts extended to include delta values and coverage; output of chip type fixed.
Sorting order retained for transcript exports.
Fixed a bug where the file chooser wouldn't open when exporting data.
Better notification when software updates are available.

As ChipInspector 2.1 is based on a more recent version of the Netbeans platform the new features are only available after downloading and installing the new version. Getting the new version via the built-in updating functionality is not possible.

July 2008: ChipInspector Release 2.0

Probe annotation is based on ElDorado 07-2008.
Improved memory management
- tiling arrays now accessible for machines with 1 GB main memory
Improved performance (up to 10-fold).
Manageable user interface.
Comprehensive positional information and annotation for all arrays.
Chip types supported:
- 54 Affymetrix arrays (including Tiling sets; ENCODE 1 and 2 are not supported)
- 9 Illumina arrays
- 6 Agilent arrays

ChipInspector 2.0 is based on a new client platform and can be installed and executed in parallel to ChipInspector 1.x.

November 2007: ChipInspector Release 1.4

In addition to Affymetrix microarrays, the following chip types are recognized:
- Agilent Chips
  - Agilent Human Promoter
  - Agilent Whole Human Genome
  - Agilent Mouse Promoter
  - Agilent Whole Mouse Genome
- Illumina BeadChips
  - Illumina Human Expression BeadChip V 2.0
  - Illumina Mouse Expression BeadChip V 1.1
Additional Affymetrix chips supported:
- Affymetrix Exon Arrays
  - Mouse Gene 1.0 ST
  - Rat Gene 1.0 ST
- Affymetrix Tiling Arrays
  - Arabidopsis Tiling 1.0 R and F
  - Chromosome 21/22 1.0 R and F
  - Chromosome 21/22 2.0 R and F
  - Drosophila Tiling 1.0 R
  - ENCODE01_4x R and F
  - ENCODE 2.0 R and F
  - Human Tiling 1.0 R
  - Human Tiling 2.0 R
  - Mouse Tiling 2.0R v2
- Affymetrix Expression Arrays
  - 500K_Sty
  - 500K_Nsp

June 2007: ChipInspector Release 1.3.5

Probe annotation is based on ElDorado 05-2007.
Position-based analysis allows
- export of significant regions,
- transcription factor binding site analysis

April 2007: ChipInspector Release 1.3

38 Affymetrix chips supported, including Human Gene 1.0 ST Array.
AGCC (Affymetrix GeneChip Command Console) compliant files supported.
Unbiased (position-based) view on tiling array data.

October 2006: ChipInspector Release 1.2

37 Affymetrix chips supported, including Promoter Tiling Arrays (Human Promoter 1.0R Array, Mouse Promoter 1.0R Array) and Exon Arrays (Human Exon 1.0 ST, Mouse Exon 1.0 ST, Rat Exon 1.0 ST).
ChipInspector results can be viewed without establishing a connection to the Genomatix server. Login to the Genomatix server is required only for starting an analysis or when annotation data from ElDorado is downloaded (e.g. for viewing more gene information).
Faster download of analysis background files.

August 2006: ChipInspector Release 1.1

34 Affymetrix chips supported, including Drosophila and Rice Gene Chip arrays, Human and Mouse Exon array.
Non-significant probe values shown in graph view.
Gene symbols shown in list view.
Possible alternative splicing shown in list view.
Gene loci without GeneIDs are utilized (increased yield).
CEL file quality assessment.

April 2006: ChipInspector Release 1.0

New or enhanced features compared to the pre-release version:

Compatibility with the Affymetrix Human Exon Array HuEx 1.0, including probe confidence information from the NetAffx center.
Presence/Absence calls to measure absolute expression values.
Probe and transcript mapping based on the current ElDorado genomes.
Graphic display of the detected gene locus and the associated probes.
(This is only feasible for newly calculated analyses and will not work with previously calculated results. This feature is not accessible to evaluation accounts.)
log 2 transformation of expression ratios.
(Please exercise caution when comparing expression ratios between the old and the new program version.)
Previously calculated results are still accessible, but to access the full features of the program, a recalculation of the analyses is inevitable.
Export data to tab-delimited or Excel formatted files.

Features of the pre-release version:

Uses single probe expression levels as input.
Supports Affymetrix CEL files.
Assigns probes correctly to transcripts and genes.
Accounts for alternative transcripts.
Eliminates normalization/interpolation problems.
Reduces false positive rates by about an order of magnitude.
Increases the number of significant features.
Applies state-of-the-art genomic knowledge.
Extracts new information by mining previous microarray experiments.
Results are directly usable as input for BiblioSphere PathwayEdition.