Bioinformatics and Functional Genomics, 2nd Edition

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
Audioof 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