Custom CDF


 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

We prepare redefined custom CDF files for different platforms for user download
NCBI Geo data can be used to test different CDFs, user name/password is public/public
Find probe content and genomic location in given probe sets
For match probe sets across different GeneChip definitions and species
So far there are four unique tools in this package, which are for celfile uploading, celfile converting, celfile splitting and Cdf probe filtering.
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.
Get the latest Custom Cdf news notification and/or use our WGAS with email notification when the job you submitted is finished.
How to upload your analysis result with custom CDF into NCBI GEO
Download Custom CDF
Query Probe Identity
Query Probe Location
Search for Probes
Query SNP on Probes
Query Probe Set Content
Download Python Package
Download R Package




We gratefully acknowledge the funding support from the Pritzker Neuropsychiatric Disorders Research Consortium, Janssen Research & Development and Hope For Depression Research Foundation.

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