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Analysis of gene expression data

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.

RNA-seq: Import and normalize (TMM method) aligned BAM files in a few well defined steps.

Affymetrix: Qlucore Omics Explorer is Affymetrix Gene Chip Compatible. It is possible to import both "*.cel" and ".chp" files directly. Both 3" arrays and WT arrays are support. You can select from several normlaization methods such as RMA and PLIER. Annotations from Affymetrix NetAffx are then automatically downloaded.

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.

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"

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.

 

 

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.