Microarray processing is a high throughput technology that provides a global view of gene expression in a cell under given condition, e.g., cell transformation, normal state, cell cycle, gene knockout, etc. The WIS Microarray Unit supports microarray experiments of both Affymetrix and Spotted Array technologies from the design through the quantification to the data analysis that makes biological sense out of your results.
The Bioinformatics Unit can help with or perform analyses of your microarray data. The current list of standard analyses follows. We can also often help with new or other kinds of non-standard analyses; please contact us if you have needs that are not covered by this list.
| Experiment | Standard analysis | Optional |
| mRNA Expression | Pre-processing: background subtraction, scaling, and
summarizing (as needed) Calculation of differentially-expressed genes Pairwise comparisons between conditions/treatments as requested |
Clustering Pathway analysis Ontologies analysis (GO) |
| ChIP-on-chip | Preprocessing, background substraction, and normalization Finding significant binding intervals Overlap between the significant intervals and genes |
|
| SNP arrays | Preprocessing, background substraction, and normalization Copy-number analysis |
Overlap between CNV and genes |
We support the following microarray software.
| Partek Genomics Suite | An application for expression analysis that integrates microarray analysis results with gene anotation resources |
| NetAffx | A web-based application to annotate Affymetrix chips |
| Spotreader | Image processing software for quantifying spotted array images |