Selecting normalization genes for small diagnostic microarrays
<p>Abstract</p> <p>Background</p> <p>Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diag...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2006-08-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/7/388 |
| _version_ | 1818387168940261376 |
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| author | Spang Rainer Jaeger Jochen |
| author_facet | Spang Rainer Jaeger Jochen |
| author_sort | Spang Rainer |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diagnostic microarrays causes new normalization problems.</p> <p>Results</p> <p>In this paper we point out the differences of normalizing large microarrays and small diagnostic microarrays. We suggest to include additional normalization genes on the small diagnostic microarrays and propose two strategies for selecting them from genomewide microarray studies. The first is a data driven univariate selection of normalization genes. The second is multivariate and based on finding a balanced diagnostic signature. Finally, we compare both methods to standard normalization protocols known from large microarrays.</p> <p>Conclusion</p> <p>Not including additional genes for normalization on small microarrays leads to a loss of diagnostic information. Using house keeping genes from the literature for normalization fails to work for certain datasets. While a data driven selection of additional normalization genes works well, the best results were obtained using a balanced signature.</p> |
| first_indexed | 2024-12-14T04:05:40Z |
| format | Article |
| id | doaj.art-3144532e2cc5457bab1ca62367ddf05d |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-14T04:05:40Z |
| publishDate | 2006-08-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-3144532e2cc5457bab1ca62367ddf05d2022-12-21T23:17:49ZengBMCBMC Bioinformatics1471-21052006-08-017138810.1186/1471-2105-7-388Selecting normalization genes for small diagnostic microarraysSpang RainerJaeger Jochen<p>Abstract</p> <p>Background</p> <p>Normalization of gene expression microarrays carrying thousands of genes is based on assumptions that do not hold for diagnostic microarrays carrying only few genes. Thus, applying standard microarray normalization strategies to diagnostic microarrays causes new normalization problems.</p> <p>Results</p> <p>In this paper we point out the differences of normalizing large microarrays and small diagnostic microarrays. We suggest to include additional normalization genes on the small diagnostic microarrays and propose two strategies for selecting them from genomewide microarray studies. The first is a data driven univariate selection of normalization genes. The second is multivariate and based on finding a balanced diagnostic signature. Finally, we compare both methods to standard normalization protocols known from large microarrays.</p> <p>Conclusion</p> <p>Not including additional genes for normalization on small microarrays leads to a loss of diagnostic information. Using house keeping genes from the literature for normalization fails to work for certain datasets. While a data driven selection of additional normalization genes works well, the best results were obtained using a balanced signature.</p>http://www.biomedcentral.com/1471-2105/7/388 |
| spellingShingle | Spang Rainer Jaeger Jochen Selecting normalization genes for small diagnostic microarrays BMC Bioinformatics |
| title | Selecting normalization genes for small diagnostic microarrays |
| title_full | Selecting normalization genes for small diagnostic microarrays |
| title_fullStr | Selecting normalization genes for small diagnostic microarrays |
| title_full_unstemmed | Selecting normalization genes for small diagnostic microarrays |
| title_short | Selecting normalization genes for small diagnostic microarrays |
| title_sort | selecting normalization genes for small diagnostic microarrays |
| url | http://www.biomedcentral.com/1471-2105/7/388 |
| work_keys_str_mv | AT spangrainer selectingnormalizationgenesforsmalldiagnosticmicroarrays AT jaegerjochen selectingnormalizationgenesforsmalldiagnosticmicroarrays |