Title: Three methods to identify differentially expressed gene sets,
ordinary least square test, Multivariate Analysis Of Variance
test with n contrasts and Random forest.
Author: Chih-Yi Chien, Chen-An Tsai, Ching-Wei Chang, and James J. Chen
Maintainer: Chih-Yi Chien <email@example.com>
Depends: R (>= 2.13.2), corpcor, foreach, multcomp, randomForest, MASS
Description: This package is a gene set analysis function for one-sided test (OLS), two-sided test (multivariate analysis of variance).
If the experimental conditions are equal to 2, the p-value for Hotelling's t^2 test is calculated.
If the experimental conditions are great than 2, the p-value for Wilks' Lambda is determined and post-hoc test is reported too.
Three multiple comparison procedures, Dunnett, Tukey, and sequential pairwise comparison, are implemented.
The program computes the p-values and FDR (false discovery rate) q-values for all gene sets.
The p-values for individual genes in a significant gene set are also listed.
MAVTgsa generates two visualization output: a p-value plot of gene sets (GSA plot) and a GST-plot of the empirical distribution function of the ranked test statistics of a given gene set.
A Random Forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes.
Packaged: 2014-06-30 03:41:28 UTC; pelly
Date/Publication: 2014-07-02 13:48:35
Title: Statistical Analysis and Data Display: Heiberger and Holland
Author: Richard M. Heiberger
Maintainer: Richard M. Heiberger <firstname.lastname@example.org>
Depends: R (>= 3.0.2), lattice, stats, grid, latticeExtra, multcomp, gridExtra (>= 2.0.0), graphics
Imports: reshape2, leaps, vcd, colorspace, RColorBrewer, shiny (>=
0.13.1), Hmisc, abind, Rmpfr (>= 0.6.0), grDevices, methods
Suggests: mvtnorm, car, Rcmdr, RcmdrPlugin.HH, TeachingDemos, microplot
Description: Support software for Statistical Analysis and Data Display (Second Edition, Springer, ISBN 978-1-4939-2121-8, 2015) and (First Edition, Springer, ISBN 0-387-40270-5, 2004) by Richard M. Heiberger and Burt Holland. This contemporary presentation of statistical methods features extensive use of graphical displays for exploring data and for displaying the analysis. The second edition includes redesigned graphics and additional chapters. The authors emphasize how to construct and interpret graphs, discuss principles of graphical design, and show how accompanying traditional tabular results are used to confirm the visual impressions derived directly from the graphs. Many of the graphical formats are novel and appear here for the first time in print. All chapters have exercises. All functions introduced in the book are in the package. R code for all examples, both graphs and tables, in the book is included in the scripts directory of the package.
License: GPL (>= 2)
Packaged: 2016-06-22 04:32:23 UTC; rmh
Date/Publication: 2016-06-23 01:13:28
Title: Interlaboratory Study
Depends: R (>= 3.1.0), multcomp, depthTools, fda.usc, MASS
Description: It performs interlaboratory studies (ILS) to detect those laboratories that provide non-consistent results when comparing to others.
It permits to work simultaneously with various testing materials, from standard univariate, and functional data analysis (FDA) perspectives.
The univariate approach based on ASTM E691-08 consist of estimating the Mandel's h and k statistics to identify those laboratories
that provide more significant different results, testing also the presence of outliers by Cochran and Grubbs tests, Analysis of variance (ANOVA)
techniques are provided (F and Tuckey tests) to test differences in means corresponding to different laboratories per each material.
Taking into account the functional nature of data retrieved in analytical chemistry, applied physics and engineering (spectra, thermograms, etc.).
ILS package provides a FDA approach for finding the Mandel's k and h statistics distribution by smoothing bootstrap resampling.
License: GPL (>= 2)
Author: Miguel Flores [aut, cre],
Salvador Naya [ctb],
Javier Tarrio-Saavedra [ctb],
Ruben Fernandez [ctb],
Rubi Arias [ctb]
Maintainer: Miguel Flores <email@example.com>
Packaged: 2016-05-23 10:48:30 UTC; MiguelA
Date/Publication: 2016-05-23 13:04:51
Title: Statistical methods for safety assessment in agricultural field
Author: Frank Schaarschmidt
Description: Collection of functions, data sets and code examples
for evaluations of field trials with the objective of equivalence assessment.
Maintainer: Frank Schaarschmidt <firstname.lastname@example.org>
Depends: gamlss, multcomp, MCPAN
Imports: mvtnorm, boot, mratios
Packaged: 2013-11-21 10:22:19 UTC; Schaarschmidt
Date/Publication: 2013-11-21 11:50:03
Title: Multiple Comparisons and Simultaneous Confidence Intervals
Author: Frank Konietschke
Maintainer: Frank Konietschke <email@example.com>
Description: With this package, it is possible to compute nonparametric simultaneous confidence intervals for relative contrast effects in the unbalanced one way layout. Moreover, it computes simultaneous p-values. The simultaneous confidence intervals can be computed using multivariate normal distribution, multivariate t-distribution with a Satterthwaite Approximation of the degree of freedom or using multivariate range preserving transformations with Logit or Probit as transformation function. 2 sample comparisons can be performed with the same methods described above. There is no assumption on the underlying distribution function, only that the data have to be at least ordinal numbers.
Depends: multcomp, mvtnorm
Packaged: 2015-03-12 13:24:37 UTC; mplacze
Date/Publication: 2015-03-12 17:09:01