logistic Principal Component Analysis for binary data (gene presence absence between 3 states)
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3 months ago
pple2202 ▴ 10

Hi all.

I have a question on logistic PCA for my data.

I have a data of gene_presence_absence following states (stateA, stateB, stateC), and I'd like to show this on Coordinate plot using logistic PCA. So that I can show genes are clustered following states, and stateA and B have similar clustering pattern. As I know, logistic PCA is used for binary data, right?

So I refer to a code on this link (https://cran.r-project.org/web/packages/logisticPCA/vignettes/logisticPCA.html), but it shows me an error ("Error in rep(1, nrow(newdata)) : Wrong factor, 'times'") . I have no idea whether I use a code incorrectly or my dataset is wrong. I set the data as same as its test data (Matrix containing binary data as numeric type, rows as a state and columns as a factor of binary data (gene's name in my case)).

Thank you for all of your comments in advance!

gene logistic PCA binary • 174 views
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