So Bioconductor will only work after you have installed these packages.Īdditionally, you will need an R-package for making graphs of the data, called ggplot2Ĭheck out our R introduction tutorial to learn how to install these packages. However, Bioconductor uses functions and object from various other R packages, so you need to install these R packages too: To analyze microarray data, you need a specific R package, called Bioconductor. 9.9 Creating a Venn diagram to compare results of multiple comparisonsĬheck out our R introduction tutorial to learn how to install R and RStudio.9.8 Creating a heat map of the DE genes.9.7 Creating lists of probe set IDs of DE genes for functional analysis.9.6 Adjusting for multiple testing and defining DE genes.8.3.2.4 Comparing raw and normalized data using MA plots.8.3.2.3 Comparing raw and normalized data using boxplots.8.3.2.2 Comparing raw and normalized data in oligo.8.3.2.1 Comparing raw and normalized data in affy.8.3.2 Comparing raw and normalized data.8.3.1 Comparing raw and background-corrected data.8.3 Checking the effect of the normalization.7.3.2 Calculate quality measures in oligo.7.3.1 Calculate quality measures in affy.7.3 Calculate quality measures to assess the quality of the data.7.2 Create plots to assess the quality of the data.7.1 Giving the samples informative names.6.3 Retrieving other types of information.6.2.4 Retrieving annotation using oligo.6.2.3 Retrieving experiment annotation using affy.6.2.2 Retrieving probe annotation using affy.6.2.1 Retrieving sample annotation using affy.6.1.2 Retrieving intensities using oligo.6.1.1 Retrieving intensities using affy.5.2 Open CEL files from newer Affymetrix Arrays (HTA, Gene ST.) using oligo.5.1 Open CEL files from 3' Affymetrix Arrays (older ones) using affy.3 Using a method from a specific package.1.5 Updating installed Bioconductor packages.1.4 Installing Bioconductor packages from source.1.3 Install Bioconductor packages from Bioconductor repository.
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