Aedín Culhane aedin@jimmy.harvard.edu Introduction to Bioc Aedín Culhane aedin@jimmy.harvard.edu http://bcb.dfci.harvard.edu/~aedin http://www.hsph.harvard.edu/research/aedin-culhane/

Bioconductor To install use script on Bioconductor Website source("http://www.bioconductor.org/biocLite.R") biocLite()

What Packages do I need? Specific to you data and analysis pipeline but for examples: Bioconductor Workshops Bioconductor Workflows

Packages Overview BioConductor web site Bioconductor BiocViews Task view Software Annotation Data Experimental Data

Main types of Annotation Packages Gene centric AnnotationDbi packages: Organism: org.Mm.eg.db. Technology/Platform: hgu133plus2.db. GeneSets and Pathway (biology level): GO.db or KEGG.db .db packages can be queried with sql or accessed using annotation package (totable, get, mget) Genome centric GenomicFeatures packages: Transriptome level: TxDb.Hsapiens.UCSC.hg19.knownGene Generic features: Can generate via GenomicFeatures biomaRt: Query web-based `biomart' resource for genes, sequence, SNPs, and etc. See http://www.bioconductor.org/help/course-materials/2011/BioC2011/LabStuff/AnnotationSlidesBioc2011.pdf

Bioconductor resources Mailing List (sign up for daily digest) Documentation, workshop/course material online Slides from talks, pdf of tutorials, R code Help available for each software package Each package MUST contain vignette (howto)‏ Other resources ww.Rseek.org www.r-bloggers.com

Vignette Tutorials, provide worked example of package Required in Bioconductor packages library("Biobase") library("GOstats") # Load package of interest openVignette()

Getting Data into R & Bioconductor Aedín Culhane aedin@jimmy.harvard.edu http://www.hsph.harvard.edu/research/aedin-culhane/

Simple Excel SpreadSheet data Simple table read.table() read.csv() scan() However more datatype specialized. See Technologies on BiocViews. http://www.bioconductor.org/packages/release/Bioc Views.html GDC - GenomicDataCommons Microarray Data- GEOquery, ArrayExpress,

A Microarray Overview

Reading Affymetrix Data May 2011 Reading Affymetrix Data library(affy) require(affy) # Alternative affybatch <- ReadAffy(celfile.path="[Location of your data]") eSet<-justRMA()

Sample R code

Other Arrays Illumina 2 color spotted arrays Other arrays Lumi package May 2011 Other Arrays Illumina Lumi package 2 color spotted arrays Limma package Other arrays http://www.bioconductor.org/help/workflows/oli go-arrays/

May 2011 R Code

More on GEOquery require(GEOquery) May 2011 More on GEOquery require(GEOquery) Let's try to load the GDS810 dataset which contains data on Alzheimer's disease at various stages of severity. GDS810<-getGEO("GDS810") The getGEO function returns an object of class GEOData. You can get a description of this class like this: help("GEOData-class") Meta(GDS810) Columns(GDS810) head(Table(GDS810))

Assessing Data Quality May 2011 Assessing Data Quality

ExpressionSet Class in R May 2011 ExpressionSet Class in R

R basics: Getting help To get help help.search(“mean”)‏ help(mean) help.search(“mean”)‏ apropos("mean") example(mean)‏ http://www.bioconductor.org/help/