Affymetrix GeneChip microarray preprocessing for multivariate analyses
نویسندگان
چکیده
منابع مشابه
Affymetrix GeneChip microarray preprocessing for multivariate analyses
Affymetrix GeneChip microarrays are the most widely used high-throughput technology to measure gene expression, and a wide variety of preprocessing methods have been developed to transform probe intensities reported by a microarray scanner into gene expression estimates. There have been numerous comparisons of these preprocessing methods, focusing on the most common analyses-detection of differ...
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MOTIVATION The defining feature of oligonucleotide expression arrays is the use of several probes to assay each targeted transcript. This is a bonanza for the statistical geneticist, who can create probeset summaries with specific characteristics. There are now several methods available for summarizing probe level data from the popular Affymetrix GeneChips, but it is difficult to identify the b...
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Motivation: Affymetrix GeneChip brand arrays require a summarization step in order to combine the information in a probe set into one value representing the expression level of the corresponding gene. Here we present a new summarization method, Distribution Free Weighted (DFW) fold change, that uses the information of fold change but does not make any distributional assumptions for the data. Re...
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MOTIVATION In the Affymetrix GeneChip system, preprocessing occurs before one obtains expression level measurements. Because the number of competing preprocessing methods was large and growing we developed a benchmark to help users identify the best method for their application. A webtool was made available for developers to benchmark their procedures. At the time of writing over 50 methods had...
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The approximately 25,000 genes in mammalian genomes can be transcribed at different levels. Measurements of gene expression for ten thousands of genes in parallel give the most comprehensive picture of steady-state levels of transcripts and is used in basic and applied research. Microarrays are the most frequently used technology for genome-wide expression profiling; from the various available ...
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ژورنال
عنوان ژورنال: Briefings in Bioinformatics
سال: 2011
ISSN: 1467-5463,1477-4054
DOI: 10.1093/bib/bbr072