Introduction | About the package | Vignettes description | Installation and loading of the limpca package | Short application on the UCH dataset | Data object | Data visualisation | PCA | Model estimation and effect matrix decomposition | Effect matrix test of significance and importance measure | ASCA decomposition | sessionInfo

Installation and loading of the limpca package | Data and model presentation | Data import and exploration | Data import and design visualization | Principal Component Analysis of row data | Log10 transformation of the data and new PCA | New PCA without the outliers | Mean agregation by aquarium and scaling | Exploration of aggregated data | Design | Example of lineplot of the responses for two observations | PCA aggregated data | Score plots | 1D Loading plots | 2D Loading plots | Scatterplot matrix of all 15 responses | GLM decomposition | Model matrix X generation | Computation of effect matrices and importances | Bootstrap test of effect significance | ASCA and APCA | ASCA | PCA decomposition of effect matrices | Contributions | Scores and loadings plots | Day effect | Treatment effect | Day:Treatment effect | Combined Day+Treatment+Day:Treatment effect | Residual matrix decomposition | Effect plots on scores | APCA | Univariate ANOVA | Parallel ANOVA modeling and FDR p-value corrections | FDR corrected p_values (q-values) | Plot ASCA loadings versus -log10(q-values) | sessionInfo | References

Introduction | Installation and loading of the limpca package | Data import | Data exploration | Design | Outcomes visualization | plotLine function | plotScatter function | plotScatterM function | plotMeans function | PCA | Application of ASCA+ and APCA+ | Model estimation and effect matrix decomposition | Model formula | Model matrix generation | Model estimation and effect matrices decomposition | Effects importance | Bootstrap tests and quantification of effects importance | ASCA/APCA/ASCA-E decomposition | ASCA | Contributions | Scores and loadings Plots | Main effects | Interaction Hippurate:Time | Combination of effects Hippurate+Time+Hippurate:Time | Model residuals | Other graphs | Scores scatter plot | 2D Loadings | Effects plot | Main effects for Hippurate | APCA | Scores Plot | Loadings plot | ASCA-E | sessionInfo | References

Introduction | Installation | Data importation | Pre-processing steps | Available datasets | Demo on the HSerum dataset | Load the data | Read the FID data file | Group Delay Correction | Solvent Suppression | Apodization | Zero Filling | FourierTransform | Zero Order Phase Correction | Internal Referencing | Baseline Correction | Negative Values Zeroing | Warping | Window Selection | Bucketing | Region Removal | Normalization | Final spectra visualisation | Session info | References