Data-analysis

The standard data analysis package comes with no additional charges and includes the following:

• manual screening of the scanned images for visible signs of artefacts (e.g. scratches, signal intensity gradients)
• generation of the chip report (.rpt) file: this file describes the main numerical parameters of the analysis performed (background levels & distribution, noise, present genes, regulated genes, array sensitivity, 3'-5' intensity bias)
• single array analysis using GCOS 1.3 software packages.
• implementation of various probe level data analysis algorithms (MAS5, RMA)
• matching of your expression data with the latest annotations derived from major genome databases (e.g. genbank, unigene, swiss-prot), plus Gene Ontology based functional annotation (GO molecular function, GO biological process, GO cellular component)
• clear data arrangement plus data export into easily accessible formats (.txt, .xls)

Data analysis with additional charges include:

• Normalization within and between slides
• Global analysis of data by clustering methods and principal component analysis
• Significance testing and identification of differentially expressed genes
• Expression profiling sample classification (support factor machines)
• Go analysis, e.g. over-represented gene ontologies and gene set enrichement
• Pathway analysis

The client will receive the appropriate analyses of the processed data and image files. Intensive data analysis will be performed in close collaboration with the client.