Chapter 9: Microarray Data Analysis
Chapter 9 describes microarray data analysis. We introduce a variety of software tools including commercial and open source packages. This web page includes .cel files that you can import into the R programming language (as described in the chapter), or into other packages. You can also do some analyzes in Microsoft Excel including scatter plots and t-tests.
| Web documents | Pages |
Description |
| Web Document 9-1 | 338 | Expression data for RNA transcripts from control and trisomy 21 brain |
| Web Document 9-2 | 338, 339, 348 | Expression data for RNA transcripts from control and trisomy 21 brain |
| Web Document 9-3 | 346 | Data from Fig. 9.8: table of 8 genes, 14 samples |
| Web Document 9-4 | 346 | Transposed data (8 genes, 14 samples) |
| Web Document 9-5 | 371 | Excel spreadsheet downloaded from NCBI GEO for dataset GDS 1761 |
| Web Document 9-6 | 371 | Excel spreadsheet with edited data from GDS 1761 |
| Web Document 9-7 | 371 | NCI60 gene expression data set |
| Web Document 9-8 | 371 | Plots of data from NCI60 data set |
| .CEL files: Expression data for RNA transcripts from control and trisomy 21 brain (7 trisomy 21, 7 control)(link to GEO dataset) |
| Down Syndrome-Cerebellum-1218-1-U133A.CEL |
| Down Syndrome-Cerebellum-1389-1- (U133A.CEL |
| Down Syndrome-Cerebellum-1478-1-U133A.CEL |
| Down Syndrome-Cerebrum-1218-1-U133A.CEL |
| Down Syndrome-Cerebrum-1389-1-U133A.CEL |
| Down Syndrome-Cerebrum-1478-1-U133A.CEL |
| Down Syndrome-Cerebrum-847-1-U133A.CEL |
| Normal-Cerebellum-1390-1-U133A.CEL |
| Normal-Cerebellum-1411-1-U133A.CEL |
| Normal-Cerebellum-1521-1-U133A.CEL |
| Normal-Cerebrum-1390-2-U133A.CEL |
| Normal-Cerebrum-1411-2-U133A.CEL |
| Normal-Cerebrum-1521-2-U133A.CEL |
| Normal-Cerebrum-1565-1-U133A.CEL |
Chapter 9 Resources |
| Powerpoint of the microarray data analysis lecture from January 2009 |
| PDF (black & white) of the handout for printing, 6 slides per page from January 2009 |
| Audio of lecture from January 2009 |
| Moodle site. This teaching site includes quizzes and readings; non-registered students can enter as guests |
| Key URLs: NCBI GEO page; UCSC; Pfam database |
This page updated January 29, 2010