I am trying to follow through this post as an exercise to find genes that are not differentially expressed. Few things in this post does not work [anymore]. Can somehow help ?
1. DESeqSummarizedExperimentFromMatrix. #does not work #Instead I use the `DESeqDataSetFromMatrix` to load the data and I get this error. #This is the warning I get. Note: levels of factors in the design contain characters other than letters, numbers, '_' and '.'. It is recommended (but not required) to use only letters, numbers, and delimiters '_' or '.', as these are safe characters for column names in R. [This is a message, not an warning or error]
More Importantly, the following command yeilds null.
betaSE <- mcols(rowData(dse))$SE_conditionuntreated