**40**wrote:

I stabilize my data with rlog and then plot PCA with the DESeq proposed method.

`dds = DESeqDataSetFromMatrix(countData=histone_m, colData=Design, design=~condition)`

cds=estimateSizeFactors(dds)

met = rlog(dds)

data <- plotPCA(met, intgroup=c("condition"), returnData=TRUE)

percentVar <- round(100 * attr(data, "percentVar"))

myPlot = ggplot(data, aes(PC1, PC2, color=name)) +

geom_point(size=3) +

xlab(paste0("PC1: ",percentVar[1],"% variance")) +

ylab(paste0("PC2: ",percentVar[2],"% variance"))

Then I decided to do a normal pca from r:

`met =assay(met)`

pca<- prcomp(t(met))

screeplot_percent(pca)

col=c("red","pink","black","blue")

idx <- seq_len(3)

print(splom(pca$x[,idx], col=col,pch=19))

Function for screeplot:

`screeplot_percent <- function(x, npcs = min(10, length(x$sdev)), ...) {`

idx <- seq_len(npcs)

sum_var <- sum(x$sdev ^ 2)

vars <- 100 * (x$sdev[idx] ^ 2 / sum_var)

cumvar <- cumsum(vars)

barplot(vars, width = 0.9, space = 0.1, names.arg = idx, ylim = c(0, 100),

xlab = "Principal Component", ylab = "Percent Variance",

xaxp = c(1, npcs, npcs - 1), las = 1)

lines(x = idx - 0.5, y = cumvar, type = "b", lty = 2)

legend("bottomright", legend = c("Proportion", "Cumulative"), lty = c(1, 2),

pch = c(19, 1))

}

red -> WEN1

pink -> WEN3

black -> WNN1

blue -> WNN3

In fact PCA plots differ a bit and screeplot differ a lot. However, I do not understand why.

As you see WEN3 and WNN3 are quite apart on the second plot in comparison to the first plot. Additionally, the scale on the y-axis and x-axis is different. What is the reason for this?

Also my screeplot tells me that PC1 explains app. 75% of variance whereas ggplot claims 87%.

**17k**• written 2.5 years ago by tonja.r •

**40**