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DNA Methylation

Key functionality

In Qlucore Omics Explorer a number of different analyses can be done. For DNA Methylation data the following functionality will be of specific interest

  • Check data for outliers by visual inspection using sample Principal Component Analysis (PCA) plots.
  • Perform statistical filtering using ANOVA to enhance results. Unwanted dependencies can be removed with one mouse click.
  • Generate a list of genes that classifies data based on a selection of statistical tests: f-test, t-tests or regression.
  • Present results using for instance heatmaps or PCA plots.

 

Platform specific data import

Qlucore Omics Explorer supports data import from several sources. If you are using an array from the companies listed below, a brief description of the required import steps is also provided. 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.

Illumina: Data from Golden Gate Cancer Panel Infinium27 HumanMethylation BeadChip and Infinium HumanMethylation450 BeadChip can be extracted by using the Genome Studio Methylation module. Data can be exported in various formats which are easily imported into Qlucore Omics Explorer. See the Illumina (www.illumina.com) product documentation on how to export a normalized ".txt" file. Start Qlucore OE and import the file using the Open command from the File menu and then select the Import Wizard.

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.

 

General data import

The Qlucore Import Wizard guides you through import of both data and annotations from many platforms and instruments. You need to start the work with a file with one of the following extensions, .txt, .csv or .tsv. The data should be normallized according to the instrument manufacturers instructions. Open your file from Qlucore Omics Explorer and select the Import Wizard.