Gordon Smyth
August 16, 2005
Walter and Eliza Hall Institute of Medical Research
This laboratory explores some of the features of the limma package for assessing differential expression in microarray experiments. Examples are included of cDNA two-color microarrays and Affymetrix one-channel microarrays. Some pre-processing issues are also discussed for two-color arrays.
Exercise | Platform | Design | Topics covered |
apoAI data | cDNA | Two group comparison with common reference | Introduction to linear models. Obtaining empirical Bayes statistics. Getting lists of differentially expressed genes. |
integrin beta7 data | cDNA | Direct comparisons with dye-swaps | Data entry for two color data. Highlighting control probes. Exploring different background correction methods. Allowing for genewise dye effects. |
Estrogen data | Affymetrix | 2x2 Factorial | More on linear models. Use of contrasts. Venn diagrams. Linking gene lists to annotation information on the internet. Gene set tests. |
Drosophila embryogenesis dataset | Affymetrix | Time course with series-level replication | Time course analysis using linear models and moderated F-statistics. |
Please check whether you already have the "Drosophila Embryo" and "Estrogen" packages from the Required Software. (These data sets are stored within R packages.)
The handouts in pdf can be accessed here: lab
handouts
Please install these packages before attempting to
repeat the lab exercises. Note: if you don't have write
permission to the system library directory of your R
installation, you can use the .libPaths() function with
something like .libPaths("C:/mylibdir")
before you run install.packages()
(or
equivalent) to install the packages in a customized
directory location.
A local cache of packages is here: Local Package Cache
Package |
Windows |
MacOS X |
Source |
limma_2.0.4 |
|||
statmod_1.2.0 |
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affy_1.6.7 |
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Biobase_1.5.12 |
|||
hgu95av2_1.8.4 |
|||
hgu95av2cdf_1.5.1 |
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xtable_1.2-5 |
You should be running R 2.1.0 or 2.1.1 and limma 2.0.4. A good way to get started is to open up the Limma User's Guide:
library(limma)
If you're using Windows, just use the drop-down menu "Vignettes". Otherwise, type
limmaUsersGuide()