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Publication Detail
G-spots cause incorrect expression measurement in Affymetrix microarrays
Abstract
Background: High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in that gene’s probe set will provide a consistent message signifying the gene’s presence. We have tested this expectation by examining the correlations between probes using the data on thousands of arrays that are available in the NCBI Gene Expression Omnibus (GEO) repository. Results: We have identified probes that are not well-correlated with the other probes in their probeset but nevertheless are highly correlated with probes in other probesets. The common element of these highly correlated probes is that they contain a G-spot (a sequence of four or more guanines). Conclusions: Since these G-spot probes generally show little correlation with the other members of their probesets they are not fit for purpose and their values should be excluded when calculating gene expression values. This has serious implications, since more than 40% of the probesets in the HG-U133A GeneChip contain at least one such probe. Future array designs should avoid these untrustworthy probes.
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