The microarray menus provide facilities for the design and analysis of microarray experiments. Microarray experiments are used in genetics to screen RNA samples for tissues/cell cultures/individuals against libraries of DNA/RNA samples/fragments.
Two Channel Microarrays
The microarray menus have been designed so that you can progress easily through each step of an analysis. For example, the first submenu is for designing an experiment. This is followed by a submenu for importing data and then calculating log-ratios. Further submenus are available for exploring the data and then normalizing. The Analysis submenu can be used to estimate the effects and perform empirical Bayes estimation to add power from the parallelism of the many probes. The False Discovery rate can then be accessed to aid in deciding how many probes to follow up. The final two submenus can be used to graphically visualize the results and to cluster probes and targets to look at groups or for structure in the experiment.
Design
- Two Channel Microarray Design
- Data
- Open Microarray Data Files
- Calculate
- Microarray Log-Ratios
- Explore
- Histograms
- Density Plot
- 2D Plots
- Spatial Plot
- Normalize
- Normalize Two Channel Microarray data
- Analysis
- Estimates from Log-Ratios
- Empirical Bayes Estimates
- False Discovery Rate using Mixture Model
- Display
- Volcano Plot
- Q-Q plot
- Cluster
- Cluster Probes/Genes
- Cluster Targets/Slides
- Two-way Clustering
Click here to view an example of how the menus can be used to analyse a two channel microarray experiment.
One Channel Microarrays
- Data
- Open Microarray Data Files
- Calculate
- Calculate Affymetrix Expression Values
- Explore
- Histograms
- Density Plot
- Spatial Plot
- Normalize
- One channel Quantile Normalization
- Analysis
- One Channel ANOVA
- Empirical Bayes Estimates
- False Discovery Rate using Mixture Model
- Display
- Volcano Plot
- Q-Q plot
- Cluster
- Cluster Probes/Genes
- Cluster Targets/Slides
- Two-way Clustering
Click here to view an example of how the menus can be used to analyse an Affymetrix microarray experiment.