PCA:Multidrug

Variables representation

See also this page for more details about correlation circles (2D and 3D plots).

## Representing the variables on correlation circles for the first 2
## principal components

plotVar(result, comp = c(1, 2), var.label = TRUE, cex = 0.7)

## Or on 3 principal components
plot3dVar(result, var.label = TRUE, cex = 0.6)

Biplot representation

A biplot simultaneously represents the samples and the variables on the same plots. It is often used to display PCA results.

## Biplot for the first 2 principal components, set choices = c(1, 3)
## to display it for principal components 1 and 3
## This function has been borrowed from the stats package (biplot.princomp)
biplot(result, cex = 0.6, xlabs = paste(multidrug$cell.line$Class, 1:nrow(X)))

References

  • Scherf U., Ross D. T., Waltham M., Smith L. H., Lee J. K., Tanabe L., Kohn K. W., Reinhold W. C., Myers T. G., Andrews D. T., Scudiero D. A., Eisen M. B., Sausville E. A., Pommier Y., Botstein D., Brown P. O. and Weinstein J. N. (2000) A Gene Expression Database for the Molecular Pharmacology of Cancer. Nature Genetics 24, pp 236-244.
  • Szakács G., Annereau J.-P., Lababidi S., Shankavaram U., Arciello A., Bussey K.J., Reinhold W., Guo Y., Kruh G.D., Reimers M., Weinstein J.N. and Gottesman M.M. (2004) Predicting drug sensitivity and resistance: Profiling ABC transporter genes in cancer cells. Cancer Cell 4, pp 147-166.
  • Weinstein J.N., Kohn K.W., Grever M.R., Viswanadhan V.N., Rubinstein L.V., Monks A.P., Scudiero D.A., Welch L., Koutsoukos A.D., Chiausa A.J. et al. (1992) Neural computing in cancer drug development: Predicting mechanism of action. Science 258, pp 447-451.

A further analysis using rCCA to integrate the ABC transporters and the compounds:

  • González I., Déjean S., Martin P.G.P., Gonçalves O., Besse P. and Baccini A. (2009) Highlighting Relationships Between Heteregeneous Biological Data Through Graphical Displays Based On Regularized Canonical Correlation Analysis. Journal of Biological Systems 17(2), pp 173-199. [link]
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