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Jianpeng Ma(02-25-05)
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Zhijin Wu (02-24-05)
Zhijin Wu (02-24-05)
Zhijin Wu (02-24-05)
PhD. Biostatistics Department, John Hopkins UniversityTitle: A Model-based Background Adjustment for Oligonucleotide Expression Arrays.[25]
Abstract:
High density oligonucleotide expression arrays are widely used in many areas of biomedical research. Affymetrix GeneChip arrays are the most popular. In the Affymetrix system, a fair amount of further pre-processing and data reduction occurs following the image processing step. Statistical procedures developed by academic groups have been successful at improving the default algorithms provided by the Affymetrix system.
Affymetrix GeneChip arrays use short oligonucleotides to probe for genes in an RNA sample. Typically each gene will be represented by 11-20 pairs of oligonucleotide probes. The first component of these pairs is referred to as a perfect match probe and is designed to hybridize only with transcripts from the intended gene (specific hybridization). However, hybridization by other sequences (non-specific hybridization) is unavoidable. Furthermore, hybridization strengths are measured by a scanner that introduces optical noise.
Therefore, the observed intensities need to be adjusted to give accurate measurements of specific hybridization.We illustrate the practical consequences of not adjusting appropriately for the presence of nonspecific hybridization and provide a solution based on our background adjustment procedure. This solution greatly improves the performance of the technology in various practical applications.
- The procedures before the final data we have, like background adjustment, normalization, still have lots of problems and are not totally solved.
- Her method(GCRMA) seems to be able to capture low-concentration genes, which are typical for transcription factors. Maybe it's a good method when i deal with transcriptors.
- No matter what quality these low-level methods have achieved, the discovery of biological results based on the data output by them should keep going. They will affect the scope, but not the idea. But I should watch these things, their breakthrough means reduction of my filtering.
Yu Huang 2006-03-25
Gene Regulatory Networks Special Feature (PNAS)