1. Aedín Culhane aedin@jimmy.harvard.edu
Introduction to Bioc
Aedín Culhane

2. Bioconductor To install use script on Bioconductor Website
source("
biocLite()

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

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

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
library("Biobase")
library("GOstats") # Load package of interest
openVignette()

8. Getting Data into R & Bioconductor
Aedín Culhane

9. Simple Excel SpreadSheet data
Simple table
read.table()
read.csv()
scan()
However more datatype specialized. See Technologies on BiocViews.
Views.html
GDC - GenomicDataCommons
Microarray Data- GEOquery, ArrayExpress,

10. A Microarray Overview

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

12. Sample R code

13. 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
go-arrays/

14. May 2011
R Code

15. 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))

16. Assessing Data Quality
May 2011
Assessing Data Quality

17. ExpressionSet Class in R
May 2011
ExpressionSet Class in R

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