I am interested in knowing the proportion of variance that my components describe in the Principle Component Analysis in DESeq2. I have successfully been able to do the rlogtransformation and the variancestablizedtransformation, and plotPCA to see the clustering of my samples. Now I am interested in the std dev, proportion of variance, and cumulative proportion of this PCA... similar to the summary if you ran:
> pca <- princomp(data, scores=TRUE, cor=TRUE)
> summary(pca)
Any suggestions for getting this information, or for changing the rld SummarizedExperiment into a regular data frame or matrix so that I can run princomp and summary as usual.
> pca <- princomp(data, scores=TRUE, cor=TRUE)
> summary(pca)
Any suggestions for getting this information, or for changing the rld SummarizedExperiment into a regular data frame or matrix so that I can run princomp and summary as usual.
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