Statistics for genomic data analysis
MATH-474
This file is part of the content downloaded from Statistics for genomic data analysis.
- Announcements (Forum)
- CRAN: The Comprehensive R Archive Network (URL)
- R Studio downloads page (URL)
- Quick-R home page (URL)
- R Markdown: The Definitive Guide (URL)
- R Markdown lessons from R Studio (URL)
- knitr with R Markdown - Karl Broman's website (URL)
- BioConductor Case Studies (URL)
20 February
Week 1: Molecular biology and technology background
VIDEO ONLY - NO IN-PERSON MEETING
VIDEO ONLY - NO IN-PERSON MEETING
- Video Lecture 1a (URL)
- Video Lecture 1b (URL)
- Lecture 1 (File)
- TP 0 (File)
- TP 1 (Page)
- Q+A lecture/tp 1 (Forum)
27 February
Week 2: Quantifying expression for Affy chips (RMA); IDE: Identifying differentially expressed (DE) genes
- Video Lecture 2a (URL)
- Video Lecture 2b (URL)
- Lecture 2 (File)
- Irizarry et al. RMA paper (optional) (URL)
- limma method paper (optional) (URL)
- B-stat paper (optional) (File)
- Ben Bolstad's PhD dissertation (optional) (File)
- TP 2 (File)
- DAFLcel.zip (File)
- Q+A lecture/tp 2 (Forum)
6 March
Week 3: Quality assessment for Affy chips; robust regression and affyPLM
- Video Lecture 3a (URL)
- Video Lecture 3b (URL)
- Lecture 3 (File)
- TP 3 (File)
- DAFL cel files (File)
- Paper comparing quality measures (URL)
- Q+A lecture/tp 3 (Forum)
13 March
CLASS AND LAB CANCELLED
20 March
Week 5: Experimental design; linear modeling
- Video Lecture 4a (URL)
- Video Lecture 4b (URL)
- Lecture 4 (File)
- Linear Models in R (File)
- Stop Ignoring Experimental Design ... (File)
- Linear Statistical Models (File)
- TP 4 (File)
- PT cel files (File)
- Q+A lecture/tp 4 (Forum)
27 March
Week 6: Hypothesis testing review; multiple testing; permutation test
- Video Lecture 5a (URL)
- Video Lecture 5b (URL)
- Lecture 5 (File)
- What's a p-value? (File)
- R/S graphics (File)
- latex page layout (URL)
- TP 5 (File)
- Q+A lecture/tp 5 (Forum)
3 April
Week 7: Cluster analysis
- Video Lecture 6a (URL)
- Video Lecture 6b (URL)
- Lecture 6 (File)
- TP 6 (File)
- Hierarchichal clustering in R (URL)
- Heatmaps in R (URL)
- Heatmaps in R - short tutorial (URL)
- R graph gallery - heatmaps (URL)
- Help on adding legend to heatmap (URL)
- Q+A lecture/tp 6 (Forum)
- TP 7 - Practice Exam (File)
- (Practice) Exam evaluation criteria (File)
- Exam Guidance (File)
- Additional tips for reports (File)
- Q+A tp 7 (Forum)
10 April
Week 8: Classification (optional)
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on TP 7 (practice exam)
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
- Lecture 7 (optional) (File)
- Using rpart to make classification and regression trees (URL)
- Machine learning in R (URL)
- Another example: ClassifyR package (optional) (URL)
17 April
Week 9: Annotation; Gene set testing (optional)
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on TP 7 (practice exam)
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
Easter vacation
Easter holiday
NO LECTURE OR LAB THIS WEEK;
NO OFFICE HOURS THIS WEEK
1 May
Week 10: Introduction to sequencing data, RNA-seq; generalized linear models (GLMs) (optional)
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on TP 7 (practice exam)
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
8 May
Week 11: Sequence data; DE for RNA-seq data (optional)
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on TP 7 (practice exam)
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
15 May
Week 12: Genetic association studies/GWAS (optional)
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on TP 7 (practice exam)
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
- Lecture 10 (optional) (File)
- Exam evaluation criteria (File)
- Exam Guidance (File)
- Loading public microarray data in R/BioConductor (URL)
22 May
Week 11: Genetic association studies/GWAS (optional)
Ascension: NO LECTURE OR LAB THIS WEEK; NO OFFICE HOURS THIS WEEK
Ascension: NO LECTURE OR LAB THIS WEEK; NO OFFICE HOURS THIS WEEK
Week 12: Miscellaneous topics (optional)
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on exam
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
NOTE: NO LECTURE OR LAB THIS WEEK: time to work on exam
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
Week 13: NOTE: NO LECTURE OR LAB THIS WEEK: time to work on exam
OFFICE HOURS THIS WEEK: Thursday ~11.00 - 13.00 (at least); Friday ~11.00 - 13.00 (latest - I teach a class at 13.15)
OFFICE HOURS THIS WEEK: Thursday ~11.00 - 13.00 (at least); Friday ~11.00 - 13.00 (latest - I teach a class at 13.15)
Week 14: NOTE: NO LECTURE OR LAB THIS WEEK: time to work on exam
NO OFFICE HOURS THIS WEEK - if you have questions, please email me
NO OFFICE HOURS THIS WEEK - if you have questions, please email me