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

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John Antonydas Gaspar ▴ 130

@john-antonydas-gaspar-3144

Last seen 9.6 years ago

Hello Sir or Madam, I am able to generate 3Dgraph of PCA using html fucntion at made4 package but how to go about in calculating the percentage of variance in all three Principal Components PC#1 (F1), PC#2(F2) and PC#3(F3). 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. I have attached here the 3D PCA graph generated and provided the summary(pca) from 'procomp'. Thanking you i advance, With kind regards, antony

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ADD COMMENT • link 13.6 years ago • updated 13.5 years ago John Antonydas Gaspar ▴ 130

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John Antonydas Gaspar ▴ 130

@john-antonydas-gaspar-3144

Last seen 9.6 years ago

Hello Sir or Madam, I am able to generate 3Dgraph of PCA using html fucntion at made4 package but how to go about in calculating the percentage of variance in all three Principal Components PC#1 (F1), PC#2(F2) and PC#3(F3). 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. Thanking you in advance, With kind regards, antony

ADD COMMENT • link 13.5 years ago John Antonydas Gaspar ▴ 130

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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 ... Hth Gerhard ---------------------------------------------------------------------- -- 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

ADD REPLY • link 13.5 years ago Gerhard Thallinger ▴ 180

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Hi All, How about the output of summary pca <- prcomp(USArrests, scale = TRUE) summary(pca) Good luck, steve On Mon, Oct 18, 2010 at 5:53 AM, Gerhard Thallinger < Gerhard.Thallinger@tugraz.at> wrote: > 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 ... > > Hth > > Gerhard > > -------------------------------------------------------------------- ---- > Dr. Gerhard Thallinger E-mail: Gerhard.Thallinger@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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]

ADD REPLY • link 13.5 years ago Steve Shen ▴ 330

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