QC plots

PCA plot below and interactive MDS plot in the folder deliverables or by clicking in the link MDS-Plot.

The first PC (and first dimension of MDS) splits control versus stress as expected. PC 2 splits replicate one to the others.

DEA

Differential expression analysis was performed using DESeq2. Low count genes (less than 10 counts across all samples) were filtered out. Interactive volcano plot in the folder deliverables or by clicking in the link Volcano-Plot. Hover over a gene in the volcano plot to see the gene expression level in a scatter plot on the right hand side. Dots are colored as follows:

  • red: log2fc>0.58 and fdr <= 0.05
  • blue: log2fc<-0.58 and fdr <= 0.05

No outlier sample was indicated by Cook's distance method. Shrinkage of log fold change (LFC) is useful for visualization and ranking of genes. Here LFC values are shrunk using ashr method. DESeq2 outputs NA values for adjusted p values based on independent filtering of genes which have low counts.

The table below show the number of DEGs.

## 
## out of 10770 with nonzero total read count
## adjusted p-value < 0.05
## LFC > 0.58 (up)    : 155, 1.4%
## LFC < -0.58 (down) : 5, 0.046%
## outliers [1]       : 3, 0.028%
## low counts [2]     : 0, 0%
## (mean count < 2)
## [1] see 'cooksCutoff' argument of ?results
## [2] see 'independentFiltering' argument of ?results
## using 'ashr' for LFC shrinkage. If used in published research, please cite:
##     Stephens, M. (2016) False discovery rates: a new deal. Biostatistics, 18:2.
##     https://doi.org/10.1093/biostatistics/kxw041

## quartz_off_screen 
##                 2