With Qlucore Omics Explorer the researcher can easily examine and analyze data from miRNA experiments. For miRNA profiling the following functionality will be of specific interest:
- Check data for outliers by visual inspection using sample Principal Component Analysis (PCA) plots.
- Perform statistical analysis using ANOVA.
- Remove unwanted factors (batches) with a single mouse click.
- Use hierarchical clustering or PCA to indentify subgroups.
- Generate a list of miRNA that classifies data based on a selection of statistical tests: F-test, t-tests or regression.
- Work with variable PCA plots to find correlation and networks among selected miRNA.
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.
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.
Affymetrix: Affymetrix provides the software tool Mi RNA QC for free; see www.affymetrix.com. Start the MiRNA QC tool. Load your .cel files and then start the analysis by selecting "Run analysis". When the results are presented, go to the menu item "Tables and Intensities". Display the main table and save the table as a tab separated text file. Start Qlucore OE and import the file using the Open command in the File menu and then select the Import Wizard.
Exiqon: Exiqon offers descriptions and a workflow on how to extract data from their arrays using the Agilent Feature Extractions software (see http://www.exiqon.com/microrna-array-analysis-using-feature-extraction) on its website. Follow the instructions on the Exiqon website and then continue using the instructions for Agilent above.
Illumina: Illumina provides the Genome Studio Software where the GX module handles miRNA 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 ".txt" file. Start Qlucore OE and import the file using the Open command from the File menu and then select the Import Wizard.
Life Technologies (Invitrogen): Life technologies provides the Ncode Profiler Software free; see www.invitrogen.com. It is possible to export normalized data as a tab delimited text file. Start Qlucore OE and import the file using the Open command in the File menu and then select the Import Wizard.
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.