vsn - Variance stabilization and calibration for microarray data
The package implements a method for normalising microarray intensities from single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.
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microarrayonechanneltwochannelpreprocessing
10.37 score 59 dependents 5 scripts 11k downloadssplots - Visualization of high-throughput assays in microtitre plate or slide format
This package is here to support legacy usages of it, but it should not be used for new code development. It provides a single function, plotScreen, for visualising data in microtitre plate or slide format. As a better alternative for such functionality, please consider the platetools package on CRAN (https://cran.r-project.org/package=platetools and https://github.com/Swarchal/platetools), or ggplot2 (geom_raster, facet_wrap) as exemplified in the vignette of this package.
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visualizationsequencingmicrotitreplateassay
4.08 score 1 dependents 5 scripts 566 downloadsHiiragi2013 - Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."
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experimentdatamicroarraydataqpcrdatareproducibleresearch
4.00 score 14 scriptsHiiragi2013 - Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages
This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."
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experimentdatamicroarraydataqpcrdatareproducibleresearchdatapkg
3.90 score 10 scriptsMSMB - Data sets for the book 'Modern Statistics for Biology'
Data sets for the book 'Modern Statistics for Modern Biology', S.P. Holmes and W. Huber.
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experimentdatadatapkg
3.30 scorekidpack - DKFZ kidney package
kidney microarray data
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experimentdatacancerdatakidneycancerdatamicroarraydataarrayexpressdatapkg
3.30 score 1 scriptsdavidTiling - Data and analysis scripts for David, Huber et al. yeast tiling array paper
This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.
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experimentdatagenomesaccharomyces_cerevisiae_datamicroarraydatareproducibleresearchdatapkg
2.48 score 4 scriptsdavidTiling - Data and analysis scripts for David, Huber et al. yeast tiling array paper
This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.
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experimentdatagenomesaccharomyces_cerevisiae_datamicroarraydatareproducibleresearch
2.26 score 6 scripts