[Note: the following is subject to revision.]
| Date | Topic | Reading | Homework | |||
| Sep | 4 | (1) | Overview | Ch 1 | ||
| 6 | (2) | Meiosis and recombination | ||||
| 11 | (3) | Hidden Markov models (HMMs) for QTL mapping | App D | |||
| 13 | (4) | Data diagnostics | Ch 3 | example (protected) | |||
| 18 | (5) | Genetic map construction | tech report | HW 1 (due 10/2) [Data: hw1.csv] | ||
| 20 | (6) | Interval mapping | Sec 4.1-4.2 | |||
| 25 | (7) | Selective genotyping; significance thresholds; interval estimates of QTL location; selection bias | Sec 4.3, 4.5 | |||
| 27 | (8) | Non-normal traits | Ch 5 | |||
| Oct | 2 | (9) | Experimental design and power | Ch 6 | code | HW 2 (due 10/18) [Data: hw2.csv] | |
| 4 | No lecture | |||||
| 9 | (10) | Covariates | Ch 7 | R code | |||
| 11 | (11) | Two-dimensional, two-QTL genome scans | Ch 8 | slides (pdf) | R code | hyper_demo_stuff.RData | |||
| 16 | (12) | The X chromosome | Sec 4.4 | code | |||
| 18 | (13) | Mapping multiple QTL I | Sec 7.4; Ch 9 | HW 3 (due 11/8) [Data: hw3.csv] | ||
| 23 | (14) | Mapping multiple QTL II | slides (pdf) | |||
| 25 | (15) | Multiple QTL mapping in R/qtl | R code | .RData file | HW 4 (due 11/15-ish) [hw4_data.csv | paper | hw4_data.RData | hw4_perms.RData] | ||
| 30 | No lecture | |||||
| Nov | 1 | No lecture | ||||
| 6 | (16) | Bayesian methods | ||||
| 8 | (17) | RIL and AIL | ||||
| 13 | (18) | eQTL analysis | review article | |||
| 15 | (19) | Detecting sample mix-ups in eQTL data | slides (pdf) | R/lineup package | |||
| Last modified: Tue Nov 20 12:51:35 2012 |