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New Releases
New Additions
To The Data Resource Center
News & Updates
New Releases
Command Console (AGCC) Released
Download the software from the AGCC Product Page
Support documentation is available from the AGCC Product Support Page
View on-line video training from the Affymetrix Learning Center
Fusion SDK updated to handle CNCHP and Genotyping Console 2.0 CHP files
The Fusion SDK has been recently updated in anticipation of the pending release of Genotyping Console 2.0 (GTC 2.0), scheduled to launch later this year. The latest release of the Fusion SDK (version 1.0.10) includes the following enhancements:
- Support for copy number format CHP files (using the "multi-data" CHP file format). These have CNCHP and LOHCHP extensions.
- Updated the Java source to utilize “generics”. The Java code now requires JRE1.5 and above.
- Added support in the Java code for writing CHP files.
- Added example C++ code for writing expression and genotyping CHP files.
Affymetrix Power Tools (APT) Release 1.8.5
APT version 1.8.5 is now available from the APT DevNet Page. Be sure to check out the Change Log for information about differences from previous versions. Source code is available along with pre-built binaries for several different compute platforms.
Some of the key changes with this release:
- Added 64-bit Windows Binaries
- Added apt-cel-convert
- Substantial rewrite of apt-cel-extract (including the ability to apply chipstream transformation and the ability to extract CEL
intensities without library files)
- Improved support of AGCC CEL files
- Implemented new CN probe based gender calling and birdseed-dev genotype calling method
- Substantial improvement to rm-probe option in apt-probeset-summarize and apt-probeset-genotype
- APT documentation is now “live” on the APT website (see
http://www.affymetrix.com/support/developer/powertools/changelog/apt-probeset-summarize.html)
Please review the Change Log for the full run down. A more detailed announcement can be found on the APT message forum
New Copy Number Probe Gender Calling For SNP 6.0
APT 1.8.5 implements the cn-probe-chrXY-ratio_gender method. This method is more robust in the face of poor quality experiments,
relative to the em-cluster-chrX-het-contrast_gender method, which was the default for the computed_gender in earlier APT versions.
The improvement in gender calling can result in a slight improvement of genotyping accuracy of X and Y chromosome SNPs in male samples,
where optimal genotyping of sex chromosome SNPs requires use of the correct gender-dependent model type, haploid or diploid.
The gender calls, male, female or unknown, are output to the birdseed.report.txt file under the cn-probe-chrXY-ratio_gender
column. When the call from >cn-probe-chrXY-ratio_gender is selected to be the computed-gender for the genotyping algorithm, this call will also appear under the computed-gender column. The cn-probe-chrXY-ratio_gender call is based on the
cn-probe-chrXY-ratio_gender_ratio (see below).
The cn-probe-chrXY-ratio_gender method classifies genders considering only two possible cases, male: XY and female: XX and its
behavior is undefined for any sample that is neither XX nor XY. Such samples sometimes occur (for example XXX, XO, XXY, and XYY samples
occur at some low frequency, as does X chromosome mosaicism). Four gender-related columns are provided in birdseed.report.txt
to facilitate general interpretation of sex-chromosome copy number.
em-cluster-chrX-het-contrast_gender_chrX_het_rate:
The estimated heterozygosity rate (% AB genotypes) of SNPs on the X chromosome. Note that in the case of low-quality samples this estimate
can be inflated and viewed in isolation can cause a male sample to be misinterpreted as female.
cn-probe-chrXY-ratio_gender_meanX:
The average probe intensity (raw, untransformed) of a subset of X chromosome copy number probes on the SNP6.0 array
cn-probe-chrXY-ratio_gender_meanY:
The average probe intensity (raw, untransformed) of Y chromosome copy number probes on the SNP6.0 array.
cn-probe-chrXY-ratio_gender_ratio:
Gender ratio Y/X = cn-probe-chrXY-ratio_gender_meanY/ cn-probe-chrXY-ratio_gender_meanX. If Gender ratio Y/X < 0.48,
then the gender call is female. If Gender ratio Y/X > 0.71 then the gender call is male. Otherwise the gender call is unknown.
Simple scatter plots show locations of the XY and XX individuals. Samples with unusual genders are expected to fall outside of the two main
clusters indicating possible deviations from normal sex chromosome copy numbers.
New Additions to the Data Resource Center
Tiling/Regulation Data
Affymetrix recently announced the launch of the
GeneChip® Drosophila Tiling 2.0R Array, a newer and more complete version of the Drosophila Tiling Array.
The new design incorporates important regions in the heterochromatin and is based on the latest build of the Berkeley
Drosophila Genome Project (build 5).
Sample data from a whole transcriptome experiment for this and the previous generation Drosophila tiling array are
available in the
Data Resource Center.
Whole Transcript Gene Expression Data for Mouse & Rat
Affymetrix recently announced the release of two new arrays in the whole transcript family of gene expression products. The
GeneChip® Mouse Gene 1.0 ST Array
and the GeneChip® Rat Gene 1.0 ST Array
are now available. Please visit the
Gene 1.0 ST Array Sample Data Page at the Affymetrix Data Resource Center, or download the GCOS formatted CEL files directly here -
mouse &
rat.
News & Updates
Alternative SNP 5.0 Library File Added
Affymetrix is providing alternative, updated CDF files, named GenomeWideSNP_5.r2.cdf and GenomeWideSNP_5.r2.Full.cdf, for the Affymetrix genotyping array - Genome-Wide Human SNP Array 5.0.
The updated SNP 5.0 CDF files provide uniform access to the Copy Number content by presenting "one probe per probeset" in both the full and default updated CDF files. This uniform access applies to both Affymetrix genotyping arrays with Copy Number content-Genome-Wide Human SNP Array 5.0 and Genome-Wide Human SNP Array 6.0. The default SNP5.0 CDF; GenomeWideSNP_5.cdf, which does not present any copy number probes, has been updated to "one probe per probeset" in GenomeWideSNP_5.r2.cdf. The full SNP5.0 CDF; GenomeWideSNP_5.Full.cdf, which presents copy number probes grouped in "one probeset per Nsp fragment", has been updated to "one probe per probeset" in GenomeWideSNP_5.r2.Full.cdf.
There is no change to the SNP probeset content in either GenomeWideSNP_5.r2.cdf or GenomeWideSNP_5.r2.Full.cdf.
The updated SNP 5.0 CDF files are available on NetAffx Download Utility and the Genome-Wide Human SNP Array 5.0 support page for download.
Tiling Array Library File updates to NCBIv36 in December
Tiling Library file update for Human, Mouse and C. elegans arrays will be released in December 2007. For mouse and human whole genome and promoter tiling arrays, BPMAP files will be available to update the probe coordinates to NCBIv36. C. elegans arrays will be provided to UCSC build Ce4. The release will be announced on the NetAffx Cover page and the files will be available through the individual Tiling Array Support Pages and the tiling array library file update page.
Binary format for Copy Number Data Established
With the pending launch of Genotyping Console 2.0, Affymetrix will store the output of the Copy Number/LOH algorithms for the Genome-Wide Human SNP Array 6.0 arrays in a binary formatted CNCHP file. For the Mapping arrays, Affymetrix will store the output of the Copy Number algorithm in a binary formatted CNCHP file. The results of LOH analysis will be stored in a binary formatted LOHCHP file.
The latest version of the Fusion SDK(above) will support the parsing of these files. For those interested in the file format documentation, it is available at File Formats.
NetAffx Headers to be Altered in March 2008 for IVT expression files
Starting with NetAffx Annotation Update 25 in March 2008, the 3'IVT NetAffx Annotation Files will have informative headers that will help users better document their annotation sources.
The new 3'IVT headers are similar to those already provided for Exon, Gene and Mapping Array Annotation Files. The headers are compatible with Expression Console and Affymetrix Power Tools (APT). The headers will continue to follow the APT convention with comments preceeded by "##" characters and key-value pairs preceeded by "#%". As you can see in the example below, the headers will provide genome build, timestamp, file format and file format information.
For questions or comments regarding the 3'IVT informative headers, please contact the netaffx staff at netaffxFeedback@affymetrix.com.
##For information about the Annotation file content, please see the bundled README file.
#%create_date=Wed Mar 12 10:52:51 PDT 2007
#%chip_type=HG-U133_Plus_2
#%genome-species=Homo_sapiens
#%genome-version=hg18
#%genome-version-ucsc=hg18
#%genome-version-ncbi=36.1
#%genome-version-create_date=2006-03
#%netaffx-annotation-date=2007-11
#%netaffx-annotation-netaffx-build=25
#%netaffx-annotation-tabular-format-version=1.1
Updated GeneChip-compatible specifications
Affymetrix has updated the GeneChp-compatible specifications. The new version is dated 01 Nov 2007 which replaces the Feb. 2007 version.
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