This tutorial will illustrate how to:
- Import Affymetrix CEL files and check quality
- Add attributes describing the sample groups
- Perform exploratory analysis using the PCA scatter plot
- Find differentially expressed genes using ANOVA
- Generate a list of genes of interest
- Add annotations to the gene list
Note: the workflow described below is enabled in Partek Genomics Suite (PGS) version 7.0. Please contact the Partek Licensing Team at licensing@partek.com to request this version or update the software release via Help > Check for Updates from the main toolbar. The screenshots shown below may vary across platforms and across different versions of PGS.
Description of the Data Set
Down syndrome is caused by an extra copy of all or part of chromosome 21; it is the most common non-lethal trisomy in humans. The study used in this tutorial revealed a significant upregulation of chromosome 21 genes at the gene expression level in individuals with Down syndrome; this dysregulation was largely specific to chromosome 21 only and not to any other chromosomes. This experiment was performed using the Affymetrix GeneChip™ Human U133A arrays. It includes 25 samples taken from 10 human subjects and 4 different tissues.
The raw data for this study is available as experiment number GSE1397 in the Gene Expression Omnibus: http://www.ncbi.nlm.nih.gov/geo/.
Data and associated files for this tutorial can be downloaded by going to Help > On-line Tutorials from the PGS main toolbar. The data can also be downloaded directly from: http://www.partek.com/Tutorials/microarray/Gene_Expression/Down_Syndrome/Down_Syndrome-GE.zip.
If you need additional assistance with this data set, email us at support@partek.com or contact the Partek Technical Support staff at:
North America
(9:00 a.m. - 5:00 p.m. CST)
+1-314-884-6172
Europe
(9:00 a.m. - 5:00 p.m. GMT)
+44 2071 930426 or +1.314.884.6173
Asia/Australasia
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+65 6808 8706
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