1. Overview of Bioconductor
Aedín Culhane

2. Bioconductor
Biannual release (normally April, October) to coincide with R release.
Current: Bioconductor 2.9
(release coincide with R 2.14)
To install use script on Bioconductor Website
source("
biocLite()

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

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

5. 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

6. 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

7. Vignette Tutorials, provide worked example of package
Required in Bioconductor packages
Written in Sweave (Leisch, 2002).
LATEX dynamic reports in which R code is embedded and executable
All R code in vignette is checked (and executed) by R CMD check
library("Biobase")
library("GOstats") # Load package of interest
openVignette()

8. S4 classes and ExpressionSet
Within Bioconductor, you will encounter packages are structured around S4 object- oriented programming proposed by John Chambers (developer of S)
A class provides a software abstraction of a real world object.
A method performs an action on a class
(Think of a class as a noun, and method as verb)

9. Object (S4) An object is an instance of a class.
Descriptions are stored in slots
slotNames(ob1) lists all slots in object, or use str().
To access slots
slotname(ob1), or
slot(ob1, “slotname")

10. Example: ExpressionSet
> ALL ExpressionSet (storageMode: lockedEnvironment) assayData: features, 128 samples element names: exprs protocolData: none phenoData sampleNames: LAL4 (128 total) varLabels: cod diagnosis ... date last seen (21 total) varMetadata: labelDescription featureData: none experimentData: use 'experimentData(object)' pubMedIds: Annotation: hgu95av2
library(ALL) data(ALL) slotNames(ALL) phenoData(ALL) class(ALL) ?ExpressionSet

11. Method which act on a S4 class
showMethods(class= "ExpressionSet") getMethod("write.exprs", "ExpressionSet") Or if you wish to see how the package really works, download and look the source code

12. Getting Data into R & Bioconductor
Aedín Culhane

13. Simple Excel SpreadSheet data
Simple table
read.table()
read.csv()
scan()
However more datatype specialized. See Technologies on BiocViews.
ews.html
Large data files. Also see

14. Some common data types
Microarray
SNP
NGS
May 2011

15. A Microarray Overview

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

17. Sample R code

18. ExpressionSet Class in R
May 2011

19. Assessing Data Quality
May 2011

20. Public Microarray Data
ArrayExpress
21997 Studies (622,617 profiles,)
GEO
22,735 Studies (558,074 profiles)
Statistics May 2011

21. R Code
May 2011

22. 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))
May 2011

23. Affy SNP Arrays
May 2011

24. Process – Affy SNP Arrays (Oligo package)
May 2011

25. Other Arrays Illumina 2 color spotted arrays Other arrays Lumi package
Limma package
Other arrays
igo-arrays/
May 2011

26. Next Generation Sequencing Data

27. R Code
May 2011

28. Exercise Install the library GEOquery
Download the dataset GSE1297 using getGEO
This data will be downloaded as an eSet, so to see the expression data and phenoData, use pData and exprs
Use ArrayQualityMetrics to Assess the data quality of these data
May 2011

29. R basics: Getting help To get help help.search(“mean”)‏
help(mean)
help.search(“mean”)‏
apropos("mean")
example(mean)‏

30. With thanks to
May 2011