Easy Microarray Data Analysis

We propose both a clear analysis strategy and a selection of tools to investigate microarray gene expression data. The most usual and relevant existing R functions were discussed, validated and gathered in an easy-to-use R package (EMA) devoted to gene expression microarray analysis. These functions were improved for ease of use, enhanced visualisation and better interpretation of results.


Changes in EMA1.3.2

  • test.LC Add the 'global' parameter to specify if one want to perform a F test of the global hypothesis H0=0, or to test each contrast simultaneously

  • normAffy Add the fast argument for GCRMA normalisation

  • ordinal.chisq Chisq test for ordinal values

  • New utilities intersectg setdiffg

  • plot.sample Allow vector as input. Transformation in matrix.

  • expFilter Add p parameter to keep the probes if at least p*ncol(data) of its values is higher than the threshold

  • clustering.plot Remove pdf option Change the margin values. Calculate the margins taking into account the names and names.sup parameters

Changes in EMA1.3.1

  • clust.dist.R Changes in correlation function

  • plotSample.R Add ellipses in the graphical output

  • clustering.plot.R Bug in heatmap legend Stopifnot colnames data

  • km Graphical options changed

  • clustering.plot.R lab and lab.sup can be data.frame, casting to matrix is done manually new option legend.pos allows the user to choose the legend position

  • genes.selection the user can specify the quantile to be computed to filter the genes

Changes in EMA1.2

  • Add NAMESPACE file and update DESCRIPTION file

  • Hide the following internals functions : clust.dist, dice, FWER.Bonf, goReport, GSA.correlate.txt, htmlresult, jaccard, keggReport, MFAreport, qualitySample

  • Remove the following functions : plotExplore.R, mult.clustering.R

  • runGSA.R Add gene scores in output

  • runInTest.R Update of the plot in output

  • runHyperGO Bug ifnotfound mget function

  • runHyperKEGG Bug ifnotfound mget function

  • normAffy Bug missing function

  • vignette updated

Changes in EMA1.1

  • runPCA.R
  • Bug : plotVariable option.
  • Label is not initialized.
  • clustering.plot.R
  • A legend is added when a label is specified
  • If data is specified, an heatmap is displayed in one way clustering
  • The margins were adjusted according to the names length
  • Deals with NA values in labels
  • bioMartAnnot.R
  • Bug : outputTypeId undefined
  • probePlots.R
  • Bug : cex.axis option
  • Add a legend
  • distrib.plot.R
  • Change display using density plot instead of histogram
  • sample.plot.R
  • Legend is displayed out of the graph
  • eval.stability.clustering.R
  • Details section is added in the man page
  • test.LC.R
  • Global parameter : if someone want to perform a F test of the global hypothesis H_0=0, or to test each contrast simultaneously
  • Add multiple testing correction
  • FDR-BH.R
  • Bug in the Two-stages procedure. The error rate parameter (q) is missing.
  • runMFA.R
  • Can write a pdf report or a txt report
  • runHyperGO
  • CategorySize is used to generate all the report
  • man pages updated
  • vignette updated

Reference manual

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1.4.7 by Pierre Gestraud, 14 days ago

Browse source code at https://github.com/cran/EMA

Authors: Nicolas Servant , Eleonore Gravier , Pierre Gestraud , Cecile Laurent , Caroline Paccard , Anne Biton , Jonas Mandel , Bernard Asselain , Emmanuel Barillot , Philippe Hupe

Documentation:   PDF Manual  

GPL-3 license

Imports siggenes, affy, multtest, survival, xtable, gcrma, heatmap.plus, biomaRt, GSA, MASS, FactoMineR, cluster, AnnotationDbi, Biobase

Suggests hgu133plus2.db, lumi, GOstats, Category, vsn, GO.db, BiocGenerics, GSEABase

See at CRAN