Hi all, I'm new to R and I'm currently going through the DESeq introduction guide by Anders and Huber entitled 'Di fferential expression of RNA-Seq data at the gene level.'

Simply, I have created a PCA plot using pasillaguide data:
print(plotPCA(vsdFull, intgroup=c("condition", "libType")))

My question is how do I produce a graph showing other eigenvectors like PC3 and PC4, ideally using DESeq and gplots.

All of my values and data correspond to the original guide so I'm hoping there is some simple code to use. Thanks in advance.

Hi keaan95,

you could inspect the code for the PCA plotting function with

getMethod("plotPCA","DESeqTransform")

The line that is interesting for you is the one containing this:

        d <- data.frame(PC1 = pca$x[, 1], PC2 = pca$x[, 2], group = group,
            intgroup.df, name = colnames(object))

If you replace 1 and 2 for the columns you select, and put 3 and 4, it should do the job.