Home News • Bioconductor – Oligonucleotide Arrays #microarray #data #analysis #software

Bioconductor – Oligonucleotide Arrays #microarray #data #analysis #software

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Using Bioconductor for Microarray Analysis

Bioconductor has advanced facilities for analysis of microarray platforms including Affymetrix, Illumina, Nimblegen, Agilent, and other one- and two-color technologies.

Bioconductor includes extensive support for analysis of expression arrays, and well-developed support for exon, copy number, SNP, methylation, and other assays.

Major workflows in Bioconductor include pre-processing, quality assessment, differential expression, clustering and classification, gene set enrichment analysis, and genetical genomics.

Bioconductor offers extensive interfaces to community resources, including GEO, ArrayExpress, Biomart, genome browsers, GO, KEGG, and diverse annotation sources.

Sample Workflow

The following psuedo-code illustrates a typical R / Bioconductor session. It uses RMA from the affy package to pre-process Affymetrix arrays, and the limma package for assessing differential expression.

A top table resulting from a more complete analysis, described in Chapter 7 of Bioconductor Case Studies. is shown below. The table enumerates Affymetrix probes, the log-fold difference between two experimental groups, the average expression across all samples, the t-statistic describing differential expression, the unadjusted and adjusted (controlling for false discovery rate, in this case) significance of the difference, and log-odds ratio. These results can be used in further analysis and annotation.

Installation and Use

Follow installation instructions to start using these packages. The affy and limma packages are part of the core Bioconductor packages, and are installed automatically with

To install additional packages, such as the annotations associated with the Affymetrix Human Genome U95A 2.0, use

Package installation is required only once per R installation. View a /packagesfull list of available packages .

To use the affy and limma packages, evaluate the commands

These commands are required once in each R session.

Exploring Package Content

Packages have extensive help pages, and include vignettes highlighting common use cases. The help pages and vignettes are available from within R. After loading a package, use syntax like

to obtain an overview of help on the limma package, and the topTable function, and

to view vignettes (providing a more comprehensive introduction to package functionality) in the limma package. Use

to open a web page containing comprehensive help resources.

Pre-Processing Resources

The following provide a brief overview of packages useful for pre-processing. More comprehensive workflows can be found in documentation (available from package descriptions ) and in Bioconductor Books and monographs .

Affymetrix 3’-biased Arrays

  • Require cdf package, probe package and annotation package
  • All these packages are available from Bioconductor via biocLite()
  • Requires installation of ROOT
  • Uses data files from Affymetrix (.CDF. PGF. CLF. CSV) directly

Affymetrix Exon ST Arrays

  • Requires a pdInfoPackage built using pdInfoBuilder
  • This package collates cdf, probe, annotation data together
  • These packages are available from Bioconductor via biocLite()
  • Most cases will require a 64-bit computer running Linux and = 8Gb RAM
  • Requires installation of MySQL and Ensembl core database tables
  • Requires specially modified cdf and affy package
  • Requires a 64-bit computer running Linux and = 8 Gb RAM
  • Requires installation of ROOT
  • Uses data files from Affymetrix (.CDF. PGF. CLF. CSV) directly
  • Will run on conventional desktop computers

Affymetrix Gene ST Arrays

  • Requires a pdInfoPackage built using pdInfoBuilder
  • This package collates cdf, probe, annotation data together
  • These packages are available from Bioconductor via biocLite()
  • Requires installation of ROOT
  • Uses data files from Affymetrix (.CDF. PGF. CLF. CSV) directly

Affymetrix SNP Arrays

  • Requires a pdInfoPackage built using pdInfoBuilder
  • This package collates cdf, probe, annotation and HapMap data
  • These packages are available from Bioconductor via biocLite()
  • Not yet capable of processing CNV regions in SNP5.0 and SNP6.0 /ul

Affymetrix Tiling Arrays

  • Requires a pdInfoPackage built using pdInfoBuilder
  • This package collates data from bpmap and cif files

Nimblegen Arrays

Illumina Expression Microarrays

  • Requires lumi-specific mapping and annotation packages (e.g. lumiHumanAll.db and lumiHumanIDMapping )
  • Requires beadarray-specific mapping and annotation packages (e.g. illuminaHumanv1BeadID.db and illuminaHumanV1.db )

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