Exploration, normalization, and summaries of high density oligonucleotide array probe level data
Citations
8,324 citations
Cites background or methods from "Exploration, normalization, and sum..."
...The intensity information from the values of each of the probes in a probeset are combined together to get an expression measure, for example, Average Difference (AvgDiff), the Model Based Expression Index (MBEI) of Li and Wong (2001), the MAS 5....
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...0 Statistical algorithm from Affymetrix (2001), and the Robust Multichip Average proposed in Irizarry et al. (2003). The need for normalization arises naturally when dealing with experiments involving multiple arrays. There are two broad characterizations that could be used for the type of variation one might expect to see when comparing arrays: interesting variation and obscuring variation. We would classify biological differences, for example large differences in the expression level of particular genes between a diseased and a normal tissue source, as interesting variation. However, observed expression levels also include variation that is introduced during the process of carrying out the experiment, which could be classified as obscuring variation. Examples of this obscuring variation arise due to differences in sample preparation (for instance labeling differences), production of the arrays and the processing of the arrays (for instance scanner differences). The purpose of normalization is to deal with this obscuring variation. A more complete discussion on the sources of this variation can be found in Harteminket al. (2001)....
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...Irizarry et al. (2003) contains a more complete discussion of the RMA measure, and further papers exploring its properties are under preparation....
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...The intensity information from the values of each of the probes in a probeset are combined together to get an expression measure, for example, Average Difference (AvgDiff), the Model Based Expression Index (MBEI) of Li and Wong (2001), the MAS 5.0 Statistical algorithm from Affymetrix (2001), and the Robust Multichip Average proposed in Irizarry et al....
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...This data has been previously described in Irizarry et al. (2003)....
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6,319 citations
6,042 citations
Cites methods from "Exploration, normalization, and sum..."
...The assumptions behind the TMM method are similar to the assumptions commonly made in microarray normalization procedures such as lowess normalization [21] and quantile normalization [22]....
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5,119 citations
Cites background or methods or result from "Exploration, normalization, and sum..."
...Recent results (4,10) suggest that subtracting MM as a way of correcting for non-speci®c binding is not always appropriate....
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...In the log2 scale, the between-array standard deviation (SD) is in general ®ve times smaller than the within-probe set SD (4,7)....
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...nsf/), two sources of cRNA, human liver tissue and a central nervous system cell line (CNS), were hybridized to human arrays (HG-U95A) in a range of dilutions and proportions (4)....
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...However, the equal variance assumption does not hold for GeneChip probe level data, since probes with larger mean intensities have larger variances (4)....
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...The normalization and background correction procedures used are reported elsewhere (4,9)....
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4,822 citations
References
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