Abstract
Many commercial and custom-made microarray
formats are routinely used for large-scale gene expression surveys.
Here, we sought to determine the level of concordance between microarray
platforms by analyzing breast cancer cell lines with in situ synthesized oligonucleotide arrays (Affymetrix HG-U95v2), commercial cDNA microarrays
(Agilent Human 1 cDNA), and custom-made cDNA microarrays from a
sequence-validated 13K cDNA library. Gene expression data from the
commercial platforms showed good correlations across the experiments (r = 0.78–0.86), whereas the correlations between the custom-made and either of the two commercial platforms were lower (r
= 0.62–0.76). Discrepant findings were due to clone errors on the
custom-made microarrays, old annotations, or unknown causes. Even within
platform, there can be several ways to analyze data that may influence
the correlation between platforms. Our results indicate that combining
data from different microarray platforms is not straightforward.
Variability of the data represents a challenge for developing future
diagnostic applications of microarrays.
Original language | English |
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Pages (from-to) | 1164-1168 |
Journal | Genomics |
Volume | 83 |
Issue number | 6 |
DOIs | |
Publication status | Published - 2004 |
MoE publication type | A1 Journal article-refereed |
Keywords
- cDNA microarrays
- Oligonucleotide microarrays
- Quality control
- Breast cancer