[BioC] Percentage of Variance to be included at 3D graph of Principal Component Analysis (PCA)- made4 package

Gerhard Thallinger Gerhard.Thallinger at tugraz.at
Mon Oct 18 11:53:40 CEST 2010

Dear John,

> Please help me out with this regard. 'prcomp' provides Standard 
> deviation, Proportion of variance and Cumulative Proportion. How to 
> use them in calculating the percentage of variance at all three 
> PC level.

  The percentage of variance explained can be calculated as follows:

    pca <- prcomp(USArrests, scale = TRUE)
    pc1 <- round(pca$sdev[1]^2/sum(pca$sdev^2)*100,2)
    pc2 <- round(pca$sdev[2]^2/sum(pca$sdev^2)*100,2)
    etc ...



Dr. Gerhard Thallinger             E-mail:  Gerhard.Thallinger at tugraz.at
Institute for Genomics and Bioinformatics   Web: http://genome.tugraz.at
Graz University of Technology               Tel:        +43 316 873 5343
Petersgasse 14/V                            Fax:      +43 316 873 105343
8010 Graz, Austria                 Map: http://genome.tugraz.at/Loc.html

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