Boston Bioconductor Intermediate Training March 2008

All materials provided on this page are copyright 2008, VJ Carey, Bioconductor Foundation of N.A., Inc.; all rights reserved.

Note to students. I will try to get the updated custom packages available through this site.

Preliminaries

• preliminaries (pdf)/Rnw

Day 1

• Lecture 1 (four paradigms)(pdf)/(Rnw)
• Lecture 1insert (pathway case study)(pdf)/(Rnw)
• Exercises 1 (pdf)
• Lecture 2 (containers)(pdf)/(Rnw)
• Exercises 2 (pdf)
• Exercises 3a (GEO query)(Rnw)
• GSE 3982 phenotype data for 3a (txt)
• Exercises 3b (illumina stem cells)(Rnw)

Day 2

• Lecture 4 (annotation)(pdf)/(Rnw)
• Lecture 4.5 (differential expression)(pdf)/(Rnw)
• Lecture 5 (analysis)(pdf)/(Rnw)

Day 3

• Day 3 notes (illumina parse, affy 100k snp chip) (pdf)/ (Rnw)
• Lecture 7 Machine learning(pdf)/ (Rnw)
• Machine learning lab(pdf)/ (Rnw)
• Excerpt on aCGH/tree segmentation(Rnw)

Miscellaneous history files (zip archive), which should at some point be filtered and annotated

• (zip archive)