I am doing differential expression analyses for the first time and using DESeq2. The tutorials are great, but I have a couple niche questions that I cannot find the precise answer to.
1) If I use a truth table for my ColumnData in DESeq2 where my rows are samples and my columns are events that occur or dont occur as follow:
Event A Event B Event C
S1 1 1 0
S2 1 0 1
S3 0 0 0
S4 1 0 1
Where 1 is the column event is occurring and 0 means the event is not occurring. Can DESeq2 recognize these as binary indicators of categorical data or will it assume it as a measure?
2) I would like to create a heatmap that increases from least difference to most difference, for the respective columns selected in ColumnData, from left to right and bottom to top. How do I do this appropriately for a count matrix?
Thank you, any help is appreciated, I just want to make sure I am proceeding correctly.