SIMCA Tutorial Using Omics skin in SIMCA
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Using Omics skin in SIMCA
Background
Skins are customized user interfaces that improve the usability for the dedicated application. The Omics
skin is an add-on to SIMCA 14. Its user-friendly Analysis Wizard facilitates swift analysis of various
types of omics-related data.
Data
The dataset used deals with the study of genetically modified poplar plants based on GC/MS
measurements. Original literature reference is: Wiklund, et. al, Visualization of GC/TOF-MS-Based
Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class
Models, Analytical Chemistry, 2008, 80, 115-122. In this paper, two genetic modifications are
investigated, i.e., up-regulation and down-regulation within the PttPME1 gene. This gene is involved in
the production of pectin methyl esterase, PME, which is an enzyme that de-esterifies methylated groups
within pectin. The metabolic profile was of interest and both lines indicated several symptoms of
oxidative stress response.
This tutorial illustrates the workflow in the Analysis Wizard when comparing the up-regulated group with
the wild type group. The dataset contains N = 19 observations (plants) and K = 80 variables (resolved and
integrated GC/MS profiles).
The observations (plants) are divided in two groups:
• Reference, wild-type plant, 10 plants
• Group 1, up-regulated poplar, 9 plants
Launching the Omics skin
To use the Omics skin you must have SIMCA 14 and the Omics skin installed.
Start SIMCA and launch the skin; on the View tab, in the Skins group, click Omics.
The Omics skin comprises five tabs (File, Home, Analyze, Predict and View). For modeling, the Home
tab contains all functionality of interest to do a complete run-down of the information in your omics-data.
(In order to change back to normal appearance of SIMCA, on the View tab, in the Skins group, click
Default.)
