CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss
An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is ex...
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doaj-031bd715321e4caeb0b79b1a133fdf822020-11-25T03:55:46ZengSAGE PublishingCancer Informatics1176-93512007-01-0135563CGHregions: Dimension Reduction for Array CGH Data with Minimal Information LossMark A. van de WielWessel N. van WieringenAn algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R. http://la-press.com/article.php?article_id=47Array CGHDimension reductionTumor profilesStatistical testingFDR |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Mark A. van de Wiel Wessel N. van Wieringen |
spellingShingle |
Mark A. van de Wiel Wessel N. van Wieringen CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss Cancer Informatics Array CGH Dimension reduction Tumor profiles Statistical testing FDR |
author_facet |
Mark A. van de Wiel Wessel N. van Wieringen |
author_sort |
Mark A. van de Wiel |
title |
CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss |
title_short |
CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss |
title_full |
CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss |
title_fullStr |
CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss |
title_full_unstemmed |
CGHregions: Dimension Reduction for Array CGH Data with Minimal Information Loss |
title_sort |
cghregions: dimension reduction for array cgh data with minimal information loss |
publisher |
SAGE Publishing |
series |
Cancer Informatics |
issn |
1176-9351 |
publishDate |
2007-01-01 |
description |
An algorithm to reduce multi-sample array CGH data from thousands of clones to tens or hundreds of clone regions is introduced. This reduction of the data is performed such that little information is lost, which is possible due to the high dependencies between neighboring clones. The algorithm is explained using a small example. The potential beneficial effects of the algorithm for downstream analysis are illustrated by re-analysis of previously published colorectal cancer data. Using multiple testing corrections suitable for these data, we provide statistical evidence for genomic differences on several clone regions between MSI+ and CIN+ tumors. The algorithm, named CGHregions, is available as an easy-to-use script in R. |
topic |
Array CGH Dimension reduction Tumor profiles Statistical testing FDR |
url |
http://la-press.com/article.php?article_id=47 |
work_keys_str_mv |
AT markavandewiel cghregionsdimensionreductionforarraycghdatawithminimalinformationloss AT wesselnvanwieringen cghregionsdimensionreductionforarraycghdatawithminimalinformationloss |
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1724468183884103680 |