Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression.
BACKGROUND
There are many potential sources of variability in a microarray experiment. Variation can arise from many aspects of the collection and processing of samples for gene expression analysis. Oligonucleotide-based arrays are thought to minimize one source of variability as identical oligonucleotides are expected to recognize the same transcripts during hybridization.


RESULTS
We demonstrate that although the probes on the U133A GeneChip arrays are identical in sequence to probes designed for the U133 Plus 2.0 arrays the values obtained from an experimental hybridization can be quite different. Nearly half of the probesets in common between the two array types can produce slightly different values from the same sample. Nearly 70% of the individual probes in these probesets produced array specific differences.


CONCLUSIONS
The context of the probe may also contribute some bias to the final measured value of gene expression. At a minimum, this should add an extra level of caution when considering the direct comparison of experiments performed in two microarray formats. More importantly, this suggests that it may not be possible to know which value is the most accurate representation of a biological sample when comparing two formats.
Zhang
LanMin
L
Microarray Core Laboratory, H, Lee Moffitt Cancer Center and Research Institute, SRB2, 12902 Magnolia Drive, Tampa, Florida 33612, USA. Zhanglm@moffitt.usf.edu
Yoder
Sean J
SJ
Enkemann
Steven A
SA
D030561:Databases, Nucleic Acid; D005786:Gene Expression Regulation; D006801:Humans; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides; D020411:Oligonucleotide Array Sequence Analysis; D015345:Oligonucleotide Probes; D011506:Proteins / Q000235:genetics; D012313:RNA / Q000235:genetics; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid
D009838:Oligodeoxyribonucleotides; D015345:Oligonucleotide Probes; D011506:Proteins; D012313:RNA