Chapter: 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | App 1 | App 2
| Website | URL |
|---|---|
| The Microarray Gene Expression Data (MGED) Society | http://www.mged.org |
| Terrence Speed laboratory | http://www.stat.Berkeley.EDU/users/terry/zarray/Html/papersindex.html |
| HuGE | http://www.HugeIndex.org |
| Stanford Microarray Database | http://genome-www5.stanford.edu/MicroArray/SMD/ |
| SNOMAD | http://www.snomad.org |
| GeneTraffic software from Iobion | http://www.iobion.com |
| Partek Pro | http://www.partek.com |
| GeneSpring | http://www.sigenetics.com |
| GeneSight and Genedirector | http://www.biodiscovery.com |
| Spotfire | http://spotfire.com |
| SAM | http://www-stat.stanford.edu/~tibs/SAM |
| Cluster | http://rana.lbl.gov/EisenSoftware.htm |
| Time (t) | Behavior of gene | Raw ratio value | Log2 ratio value |
|---|---|---|---|
| t=0 | Basal level of expression | 1 | 0 |
| t=1 | No change | 1 | 0 |
| t=2 | Two-fold up-regulation | 2 | 1 |
| t=3 | Two-fold down-regulation | 0.5 | -1 |
| Paradigm | Parametric test | Nonparametric test |
|---|---|---|
| Compare one group to a hypothetical value | One-sample t-test | Wilcoxon test |
| Compare two unpaired groups | Unpaired t-test | Mann-Whitney test |
| Compare two paired groups | Paired t-test | Wilcoxon test |
| Compare three or more unmatched groups | One-way ANOVA | Kruskal-Wallis test |
| Compare three or more matched groups | Repeated-measures ANOVA | Friedman test |
| Resource | Comment |
|---|---|
| Y.F. Leung’s microarray site | |
| Stanford Microarray Database | Includes lists of software tools |
| TIGR | Various programs |
| Microarray & Data Analysis | Literature on array analysis |
| MadB | National Cancer Institute and CIT, NIH |
| Software | Company/organization |
|---|---|
| Access | Microsoft |
| Array Suite | Affymetrix |
| Array Organizing Tool (ARROGANT) | The University of Texas Southwestern Medical Center at Dallas |
| Atlas Navigator | Clontech |
| BioArray Software Environment (BASE) | |
| BioMine | |
| Cleaver | Stanford University |
| Cluster Analysis of Gene Expression Dynamics (CAGED) | Harvard Medical School |
| Cluster/Treeview | Stanford University |
| DRAGON | Kennedy Krieger Institute |
| Excel | Microsoft |
| Expression Profiler | European Bioinformatics Institute |
| GeneCluster | Whitehead Institute |
| GeneCruiser | Whitehead Institute |
| GeneSight | BioDiscovery |
| GeneSpring | Silicon Genetics |
| GeneTraffic | |
| GeneLinker | Molecular Mining |
| GeneViz | |
| J-Express | MolMine |
| Partek | Partek |
| Pathways | Research Genetics |
| S-PLUS | Insightful Corp. |
| Signficance Analysis of Microarrays (SAM) | Excel plug-in |
| SNOMAD | Kennedy Krieger Institute |
| Spotfire | |
| SPSS-Clementine | |
| STATA | |
| STATISTICA | |
| TIGR | |
| X-MINER | |
| XLSTAT | Excel plug-in |