w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Sartorius company, https://www.sartorius.com/en/products/process-analytical-technology/data-analytics-software.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/90708fdbc22d
3. Release v0.98.18 addresses:

• issue #14: "Specify lower limit to number of cross-validation segments"

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/2ae2d26e3270
3. Release v0.98.17 addresses

• issue #9: "Salience needs more info about spread"
• issue #13: "Improve calc of FWER-adjusted p-value for correlation calc"

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/ddaf84e15d06
3. Release v0.98.16 addresses

• issue #11: "correlation calculation is incorrect"
• issue #12: "calculate significance for correlation"

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/ddcc33ff3205
3. Release v0.98.15 fixes issue #8 - "only contrast chosen factor levels".

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/9a52306991b3
3. Release v0.98.14 fixes missing support for underscores in class levels.

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/06c51af11531
3. Release v0.98.13 fixes continuous-integration testing and specifies ropls package version.

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/342570ad880c
3. Release v0.98.12 merges pull requests 3 and 4

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/066b1f409e9f
3. Release v0.98.11 addresses issue 2 - center and pareto-scale data

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/7bd523ca1f9a

w4mcorcov - A Galaxy tool to present OPLS-DA contrasts

OPLS-DA Contrasts - a Galaxy tool

The OPLS-DA Contrasts Galaxy tool presents an emulation of the SIMCA® OPLS-DA® S-PLOT®.

For each pair of treatment levels, this tool plots:

• an emulation of the S-PLOT®, i.e., for each feature, the correlation of the treatment level with the "parallel component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation between the two treatment levels against the degree to which the feature influences that variation.
• two OPLS-DA® plots (scores and cross-validation) from the Bioconductor ropls package, doi:10.18129/B9.bioc.ropls.
• an analog to the S-PLOT® for orthogonal features, i.e., for each feature, the correlation of the treatment level with the "orthogonal component" of the OPLS-DA® projection of multivariate data against the covariance of the same. In other words, this is a plot of the consistency of the effect of each feature on the variation within the two treatment levels against the degree to which the feature influences that variation.

Optionally, the features plotted may be limited to those found to be significant in a univariate test.

The original SIMCA® OPLS-DA® S-PLOT® which this tool emulates is described in:

Wiklund et al. (2008). Visualization of GC/TOF-MS-Based Metabolomics Data for Identification of Biochemically Interesting Compounds Using OPLS Class Models. In Analytical Chemistry, 80 (1), pp. 115–122. doi:10.1021/ac0713510

notes

1. OPLS-DA®, SIMCA®, and S-PLOT® are registered trademarks of the Umetrics company, http://umetrics.com/about-us/trademarks.
2. This revision of 'w4mcorcov' has been deployed to the Galaxy Toolshed at https://toolshed.g2.bx.psu.edu/view/eschen42/w4mcorcov/50f60f94c034