Analysis of gene expression data
With Qlucore Omics Explorer the researcher can examine and analyze data from gene expression experiments. For gene expression analysis the following functionality will be of specific interest - Check data for outliers by visual inspection using sample Principal Component Analysis (PCA) plots.
- Investigate any structure in data using variance filtering combined with PCA.
- Perform statistical filtering using ANOVA to enhance results.
- Generate a list of genes that classifies data based on a selection of statistical tests: f-test, t-tests or regression.
- Use hierarchical clustering or PCA to identify subgroups.
- Work with Variable PCA plots to find correlation and networks among selected genes.
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Platform specific data import
Qlucore Omics Explorer supports data import from several sources, both from Next Generation Sequencing (NGS) and arrays. If you are using arrays from the companies listed below, a brief description of the required import steps is also provided. If you have NGS data please see the Support section and the FAQs. Note that Qlucore Omics Explore expects data to be normalized before input. If you have data from other sources, please see the general data import section.
Affymetrix: Qlucore Omics Explorer is Affymetrix Gene Chip Compatible. It is possible to import ".chp" files directly into Qlucore OE. Annotations from Affymetrix NetAffx are then automatically downloaded. If you start with .cel files these need to be converted to .chp files. There are several ways to do this. One is by using the Affymetrix® Expression Console program, see www.affymetrix.com. If you use the Expression Console then import the intensity files (*.cel) by creating a study and add Intensity files. Then do "Run Analysis". The .chp files are stored in the same directory as the intensity files. Start Qlucore OE and import the file using the Open command from the File menu.
Agilent: Qlucore Omics Explorer can import and normalize data generated with the Agilent Feature Extraction software. Export data using the single file option. See the features section (menu at top right) and the document How to import data for more details.
Febit: The SW delivered with the Geniom RT Analyzer, see www.febit.com, makes it possible to export data for downstream analysis. It is possible to export data as a tab separated text file. When that is done you can follow the steps described in the section "General data import" below.
Illumina: Illumina (www.illumina.com) provides the Genome Studio Software where the GX module handles gene expression data. Data can be exported in various formats which are easily imported into Qlucore Omics Explorer. See the Illumina product documentation on how to export a normalized tab separated ".txt" file. When that is done you can follow the steps described in the section "General data import"
General data import
Use generic formats: If your file match the simple or compact text file formats supported, data can be imported directly, see the features section (menu at top right) and the document How to import data for more details.
Convert manually: Most data generated from protein array experiments can easily be converted to the Qlucore platform independent data format ".gedata" or to the compact text or the simple text format supported by Qlucore Omics Explorer. The ".gedata" format allows both data and annotations in the same file, the simple text format supports data. The annotations can be imported separately. Conversion is at best done in a spread sheet program as Excel. More information about the ".gedata" and the simple and compact text formats can be found in the features section (menu at top right) and the document How to import data.