Why do I get different results for PC1 from plotPCA(DESeq2) and prcomp?

Question

[maria2019]

I have analyzed RNA-seq data with DESeq2 and am trying to plot a 3D PCA using rgl-plot3d.

I was trying to output PC1, PC2, and PC3 and then plot them. However, I realized that I get different results for PC1 (and PC2) when I try plotPCA (used with DESeq2) and prcomp.

What is the bug on my code?

dds <- DESeqDataSetFromHTSeqCount( sampleTable = sampleTable,
                                       directory = directory,
                                       design= ~group)
rld <- rlog(dds, blind=TRUE)

From DESeq2:

data <- plotPCA(rld, intgroup=c("treatment", "sex"), returnData=TRUE )
data$PC1

[1] -1.9169863 -2.0420236 -1.9979900 -1.8891056 0.9242008 1.0638140

[7] 0.6911183 1.0551864 0.9598643 -1.5947907 -1.5666862 -1.6694684

[13] -1.2523658 -1.0785239 1.3005578 2.2913536 2.5381586 2.4287372

[19] 1.7549495

Using prcomp

mat <- assay(rld)
pca<-prcomp(t(mat))
pca <- as.data.frame(pca$x)
pca$PC1

[1] -1.29133735 -2.96001734 -3.08855648 -3.51855030 -0.68814370 -0.01753268

[7] -2.31119461 -0.10533404 -1.45742308 -1.30239486 -1.36344946 -1.93761580

[13] 6.04484324 4.83113873 0.75050886 -0.14905189 2.70759465 3.43851631

[19] 2.41799979

[maria2019]

Thanks kevin, ATpoint, and Asaf. I tried the following code based on your comments and get the same result as plotPCA.

ntop <- 500
rv <- rowVars(assay(rld))
select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, length(rv)))]
mat <- t( assay(rld)[select, ] )

pca<-prcomp(mat)
pca <- as.data.frame(pca$x)
pca$PC1

[Jeremy Leipzig]

try prcomp with scale=TRUE

Answer 1

[ATpoint]

plotPCA by default uses the top 500 most variable genes prior to prcomp, and you used all genes. Check the source code of plotPCA for details, e.g. by typing getMethod("plotPCA","DESeqTransform") in R.

Answer 2

[Kevin Blighe]

Before calling prcomp() internally (HERE), the DESeq2 function pre-filters your data based on variance. There is a parameter that can be modified to indirectly disable this behaviour..

Kevin

Answer 3

[Asaf]

You got me intrigued so I looked at plotPCA code:

function (object, intgroup = "condition", ntop = 500, returnData = FALSE) 
{
    rv <- rowVars(assay(object))
    select <- order(rv, decreasing = TRUE)[seq_len(min(ntop, 
        length(rv)))]
    pca <- prcomp(t(assay(object)[select, ]))

So DESeq2 first sort the rows by variance, select the top 500 (by default) and only then call prcomp