DESEQ2 : plotPCA

Question

[ZheFrench]

My environment is R version 3.6.2 & conda 4.8.1.

Something I used to make work doesn't work anymore. It doesn't plot the PCA anymore don't know why. Any advice would be appreciate.

rld <- rlog(dds, blind=FALSE) 

pdf(paste0(c(dir_exploration,"PCA_MDS_plot.pdf"),collapse="/"))

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

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

percentVar <- round(100 * attr(data, "percentVar"))
ggplot(data, aes(PC1, PC2,  shape=condition)) +   geom_point(size=3) +
 xlab(paste0("PC1: ",percentVar[1],"% variance")) +
  ylab(paste0("PC2: ",percentVar[2],"% variance"))
dev.off()

Error I got :

Error in La.svd(x, nu, nv) : error code 3 from Lapack routine 'dgesdd' Calls: plotPCA ... .local -> prcomp -> prcomp.default
-> svd -> La.svd Execution halted

Answer 1

[ZheFrench]

Answer :

conda install -c conda-forge lapack

And on top of it I reinstalled DESeq2 with biocmanager did the trick.

[Zhilong Jia]

if not in a conda env, how to deal with it? reinstall liblapack3 does not works for me. Thank you.

solution: https://csantill.github.io/RPerformanceWBLAS/