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This package is for version 3.4 of Bioconductor; for the stable, up-to-date release version, see crossmeta.

Cross Platform Meta-Analysis of Microarray Data

Bioconductor version: 3.4

Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. A user interface makes it easy to select control and treatment samples for each contrast and study. This input is used for subsequent surrogate variable analysis (models unaccounted sources of variation) and differential expression analysis. Final meta-analysis of differential expression values can include genes measured in only a subset of studies.

Author: Alex Pickering

Maintainer: Alex Pickering <alexvpickering at>

Citation (from within R, enter citation("crossmeta")):


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## try http:// if https:// URLs are not supported


HTML R Script crossmeta vignette
PDF   Reference Manual


biocViews Annotation, BatchEffect, DifferentialExpression, GeneExpression, Microarray, OneChannel, Preprocessing, Software, TissueMicroarray, Transcription
Version 1.0.1
In Bioconductor since BioC 3.4 (R-3.3) (0.5 years)
License MIT + file LICENSE
Depends R (>= 3.3)
Imports affy(>= 1.50.0), affxparser(>= 1.44.0), AnnotationDbi(>= 1.34.4), Biobase(>= 2.32.0), BiocGenerics(>= 0.18.0), BiocInstaller(>= 1.22.3), DT (>= 0.2), data.table (>= 1.9.6), fdrtool (>= 1.2.15), GEOquery(>= 2.38.4), limma(>= 3.28.17), matrixStats (>= 0.50.2), metaMA (>= 3.1.2), miniUI (>= 0.1.1), oligo(>= 1.36.1), pander (>= 0.6.0), RColorBrewer (>= 1.1.2), rdrop2 (>= 0.7.0), stringr (>= 1.0.0), sva(>= 3.20.0), shiny (>= 0.13.2)
Suggests knitr, rmarkdown, lydata,, testthat
Depends On Me
Imports Me
Suggests Me ccmap
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