I made a PCA using the rlog matrix from DESEQ and got this plot where one of my sample groups did not group together.
Using the same matrix in Prcomp from r the samples get more clustered.
cruzi.pca <- prcomp(rldMat2,
center = TRUE,
scale. = FALSE)
g <- ggbiplot(pcobj = cruzi.pca, scale = 1, obs.scale = 1, var.scale = 1,
groups = groups, ellipse = TRUE,
circle = TRUE, var.axes = FALSE)
g <- g + scale_color_discrete(name = '')
g <- g + theme(legend.direction = 'horizontal',
legend.position = 'top')
How can I decide what plot to use? And Why a same matrix of transformed data got so differently clusted ? Thank you.