**10**wrote:

I made a PCA using the rlog matrix from DESEQ and got this plot where one of my sample groups did not group together.

plotPCA(rld, intgroup=c("condition"))

http://s3.postimg.org/whlalmp6b/Rplot03.png

Using the same matrix in Prcomp from r the samples get more clustered.

cruzi.pca <- prcomp(rldMat2,

center = TRUE,

scale. = FALSE)

library(ggbiplot)

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')

print(g)

http://s4.postimg.org/vdsax2drx/Rplot04.png

How can I decide what plot to use? And Why a same matrix of transformed data got so differently clusted ? Thank you.

**23k**• written 3.0 years ago by tiago211287 •

**10**