So I have a problem with a dataset I'm working on. Here is information about the samples.  

Three viruses at three timepoints:
Virus1_day1, Virus1_day3, Virus1_day8.
Virus2_day1, Virus2_day3, Virus2_day8.
Virus3_day1, Virus3_day3, Virus3_day8.

And mock samples at a single timepoint:
Mock_day6

Here is a link to my actual sample list.

https://justpaste.it/1admm

Essentially, using DESeq2 I want to compare each virus at each time point to the mock condition.  I can't do this because the design model isn't full rank though.  I have only a single set of mocks, from day 6, and the viruses from days 1,3, and 8.  I want to compare each virus at each time point to the mock set.  

Specifically:
Virus1_day1 vs Mock
Virus1_day3 vs Mock
Virus1_day8 vs Mock
Virus2_day1 vs Mock
Virus2_day3 vs Mock
Virus2_day8 vs Mock
Virus3_day1 vs Mock
Virus3_day3 vs Mock
Virus3_day8 vs Mock

What I've done so far is to just separate the input based on timepoint, and then do my design matrix as ~ Virus.  I really want to be able to process all of the data in a single set, however, and extract DE data for each comparison.

Can anyone help me figure out how to make the design matrix correctly specify the contrasts I'm trying to do?  Thanks very much in advance.

Why can't you combine virus and day into a single character vector using paste(), and then set this variable to "mock" for the mock samples? So you get a factor with levels: {virus1_day1, ..., virus3_day8, mock}