Oligonucleotide probes on GeneChips
are reorganized based on the
latest genome and
transcriptome information. In addition to custom CDF files for different
target definitions, GeneChips and data analysis platforms, we also
provide 1) a
probe mapping file that matches individual probes in the custom CDF
file and the corresponding Affymetrix CDF file; 2) a
grouping file that can be used to find all targets (exons,
transcripts) represented by the same probe set. The grouping file also contains the
probe set spanning range on genome or transcripts to facilitate RT-PCR primer design.
Click here for
the detailed description of these CDF files
Our publication about custom CDF:
Systematic analysis of the impact of custom CDF on GeneChip data analysis:
And some papers that cited our work
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We prepare redefined custom CDF files for
different platforms for user download |
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NCBI Geo data can be used to test different CDFs, user name/password is public/public |
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Find probe content and genomic location in given probe sets |
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For match probe sets across different
GeneChip definitions and species |
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So far there are four unique tools in this
package, which are for celfile uploading, celfile converting,
celfile splitting and Cdf probe filtering. |
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The package is designed to eliminate a list of undesirable probes from the corresponding GeneChip. Currently we provide allele-specific probe lists within this package and users can remove SNPs based on location of the allele on the probe as well as available heterozygosity information from dbSNP126.
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Get the latest Custom Cdf news notification and/or use our WGAS with email notification when the job you submitted is
finished.
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How to upload your analysis result with custom CDF into NCBI GEO |
