Schuchhardt, J., Beule, D., Malik, A., Wolski, E., Eickho#, H., Lehrach, H. and Herzel, H. (2000), Normalization strategies for cdna microarrays, Nucleic Acids Res, 28, E47.  Home/Search   Document Not in Database   Summary   Related Articles   Check

....sources of variation and allowing between slide comparisons has itself become an interesting research topic in the filed of gene expression data analysis. Various approaches have been proposed to model the systematic variations before any further data analysis such as clustering can be applied [Kerr2000, Yang2001, Schuchhardt2000, Hill2001, Tseng2001 ]. After above pre processing steps, gene expression data can be represented by a real valued expression matrix X, where the rows of the matrix are vectors forming the expression pattems of genes, the columns of the matrix represent samples from either various conditions, development steps or ....

J. Schuchhardt, D. Beule et al. "Normalization strategies for cDNA microarrays", Nucleic Acids Research, Vol. 28, No. 10, e47, 2000.

.... data are only beginning to be described [4 10] Such noise in microarray experiments may arise from non specific hybridization of the labeled samples to elements printed on the microarray, print tip effects, slide inhomogeneities, and variability in RNA isolation, purity, labeling and detection [6,9 12]. Among these, hybridization variance contributes most significantly to the overall variation [12] Non specific hybridization can be measured through the use of specificity controls on the microarray and addressed as a statistical problem [8,13] The most common strategy in microarray ....

.... weak signals arising from low transcript levels may be masked or biased by noise (non specific hybridization) Non specific hybridization is a characteristic of cDNA microarray hybridization and may be attributed to the uniform hybridization condition applied for all sequences on the chip [4,6,7]. The frequently used fold change threshold values of 2 3 to define a significant change are often arbitrarily chosen and do not take into account the statistical significance of absolute signal intensity. For example, microarray data showing a 4 fold change derived from low signal intensities ....

Schuchhardt J, Beule D, Malik A, Wolski E, Eickhoff H, Lehrach H, Herzel H: Normalization strategies for cDNA microarrays. Nucleic Acids Res 2000, 28:E47

.... chips and DNA microarrays have recently allowed researchers to simultaneously measure the expression levels of thousands of genes in a cell population [18, 3, 9, 7, 6, 17] These experiments involve a large number of error prone steps that lead to a high level of noise in the resulting data [16]. This noise raises practical questions in interpreting experimental results: How should one handle the negative observations often reported by A#ymetrix chips How should one combine multiple observations of the same transcript level into a single estimate How should one determine ratios of ....

....are unlikely. The noise model is reflected in the conditional distribution p(y x) indicating the probability of any particular chip measurement y given a true transcript level x. This noise could arise anywhere from RNA extraction to chip reading and likely results from a variety of sources [16]. The estimation techniques developed in the following sections are applicable to any noise and prior model and therefore to any gene array technology. To illustrate their application, we derived noise and prior models from data recorded with A#ymetrix Ye6100 chip sets, each set containing four ....

J. Schuchhardt, D. Beule, A. Malik, E. Wolski, H. Eickho#, H. Lehrach, and H. Herzel. Normalization strategies for cDNA microarrays. Nucleic Acids Res, 28:E47, 2000.

....18] use labelled single stranded DNA, which is reverse transcribed from cellular mRNA, rather than the mRNA itself. 3 3 Error models in expression level estimation Gene array experiments involve a large number of error prone steps which lead to a high level of noise in the resulting data [26]. Several potential sources of measurement noise are listed in Table 1. This noise raises several practical questions in interpreting experimental results. For example, how should one combine multiple observations of the same transcript level into a single estimate How should one determine ratios ....

J. Schuchhardt, D. Beule, A. Malik, E. Wolski, H. Eickho#, H. Lehrach, and H. Herzel. Normalization strategies for cDNA microarrays. Nucleic Acids Res, 28:E47, 2000.

....conditions (as measured from different samples) In fact, normalization methods have been standard procedures in mRNA biology from its very beginning. Also, improvements to the technology are suggested, like furnishing arrays with control spots that can help to compensate for spot variability (Schuchhardt et al. 2000). Most of the error introducing variables might potentially be controllable with the help of internal standards, which, however, are not yet readily available for laboratory use (Ke et al. 2000; Vu et al. 2000) However, this approach is laborious and costly, and it still might be impossible to ....

Schuchhardt, J., D. Beule, A. Malik, E. Wolski, H. Eickhoff, H. Lehrach, and H. Herzel (2000, May). Normalization strategies for cDNA microarrays. Nucleic Acids Res 28(10), E47.

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Schuchhardt,J., Beule,D., Malik,A., Wolsky,E., Eickhoff,H., Lehrach,H. and Herzel,H. (2000) Normalization strategies for cDNA microarrays. Nucleic Acids Res., 28.

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Schuchhardt, J., Beule, D., Malik, A., Wolski, E., Eickho#, H., Lehrach, H. and Herzel, H. (2000), Normalization strategies for cdna microarrays, Nucleic Acids Res, 28, E47.

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Schuchhardt,J., Beule,D., Malik,A., Wolski,E., Eichkhoff,H., Lehrach,H. and Herzel,H. (2000) Normalization strategies of cDNA microarrays. Nucleic Acids Res., 28, e47.

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J. Schuchhardt, D. Beule et al. Normalization strategies for cDNA microarrays, Nucleic Acids Research, 28:10:E47, 2000.

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Schuchhardt, J., Beule, D., Malik, A., Wolski, E., Eickh#, H., Lehrach, H., and Herzei, H., Normalization strategies for cDNA microarrays, Nucleic Acid Res., 28(10):E47, 2000.

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Schuchhardt J, Beule D, Malik A, Wolski E, Eickho# H, Lehrach H, Herzel H: Normalization strategies for cDNA microarrays. Nucleic Acids Res. 2000, 28:e47.

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J. Schuchhardt, D. Beule et al. Normalization strategies for cDNA microarrays, Nucleic Acids Research, 28:10:E47, 2000.

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Schuchhardt, J., et al.. Normalization strategies for cDNA microarrays. Nucleic Acids Res 28, E47 (2000).

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J. Schuchhardt, D. Beule, A. Malik, E. Wolski, H. Eickho#, H. Lehrach, and H. Herzel. Normalization strategies for cDNA microarrays. Nucleic Acids Res, 28:E47, 2000.

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Schuchhardt,J., Beule,D., Malik,A., Wolski,E., Eickhoff,H., Lehrach,H. and Herzel,H. (2000) Normalization strategies for cDNA microarrays. Nucleic Acids Res., 28, e47.

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J. Schuchhardt, D. Beule, A. Malik, E. Wolski, H. Eickhoff, H. Lehrach, and H. Herzel, "Normalization strategies for cDNA microarrays", Nucleic Acids Res. 28, pp. e47i-e47v, 2000.

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