Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression
<p>Abstract</p> <p>Background</p> <p>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 m...
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| Format: | Article |
| Language: | English |
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BMC
2006-06-01
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| Series: | BMC Genomics |
| Online Access: | http://www.biomedcentral.com/1471-2164/7/153 |
| _version_ | 1818230852871520256 |
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| author | Enkemann Steven A Yoder Sean J Zhang LanMin |
| author_facet | Enkemann Steven A Yoder Sean J Zhang LanMin |
| author_sort | Enkemann Steven A |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
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| format | Article |
| id | doaj.art-f2937570a9084b7c94af4091fec4e70d |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-12T10:41:05Z |
| publishDate | 2006-06-01 |
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| spelling | doaj.art-f2937570a9084b7c94af4091fec4e70d2022-12-22T00:27:03ZengBMCBMC Genomics1471-21642006-06-017115310.1186/1471-2164-7-153Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expressionEnkemann Steven AYoder Sean JZhang LanMin<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2164/7/153 |
| spellingShingle | Enkemann Steven A Yoder Sean J Zhang LanMin Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression BMC Genomics |
| title | Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression |
| title_full | Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression |
| title_fullStr | Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression |
| title_full_unstemmed | Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression |
| title_short | Identical probes on different high-density oligonucleotide microarrays can produce different measurements of gene expression |
| title_sort | identical probes on different high density oligonucleotide microarrays can produce different measurements of gene expression |
| url | http://www.biomedcentral.com/1471-2164/7/153 |
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