giCDF – Custom CDFs

Cross-Hyridizations

In this tutorial we will use new designed Chip Definition Files (CDFs) for various Affymetrix oligonucleotide microarrays.

Data:

A new set of CDFs for four different Affymetrix GeneChip arrays are presented, namely the HG-U133A, HG-U133B, HG-U133 Plus 2.0 (designed for human samples), and the Mouse Genome 430 2.0 array. The CDFs completely avoid cross-hybridizations.

Methods:

In the applied Affymetrix microarrays most probesets include probes matching transcripts of more than one gene and probes which do not match any transcribed sequence. Therefore, we created custom CDFs that are based on the information contained in the RefSeq database. This allows us to avoid redundant probesets and overcome the problem of cross-hybridizations to generate more reliable gene expression levels.

References:

- Hummert C, Mech F, Horn F, Weber M, Drynda S, Gausmann U, Guthke R (2011) Creation and Comparison of Different Chip Definition Files for Affymetrix Microarrays. Proc BIOCOMP11