Set working directory

# Set working directory
setwd("/Volumes/bioinfomatics$/jurtasun/Courses/CBW2022/LMS_RNASeq/course/exercises")
getwd()
## [1] "/Volumes/bioinfomatics$/jurtasun/Courses/CBW2022/LMS_RNASeq/course/exercises"

  1. Read in count data and sample description. Create col_data and check dimensions.

  2. Construct DESeqDataSet object using count data and sample description.

  3. Perform rlog and vs transformation on the

  4. Draw a heatmap of count matrix based on the top 40 highly expressed genes using rlog and vst data.

  5. Generate a SDM to see the clustering of count data

  6. Perform the Principal Component Analysis using rlog method and find out the % significance values of first two principal components

  1. Repeat the PCA, this time using VST method and compare the plots with the ones obtained using rlog method.