SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   How can I make a valid design for this data in DESeq2? (http://seqanswers.com/forums/showthread.php?t=77693)

aprice67 08-22-2017 10:36 AM

How can I make a valid design for this data in DESeq2?
 
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 the actual sample information

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 with something like,
Code:


results(dds, contrast=c("Virus","mock","ACali09"),alpha=signif_cutoff)

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.


All times are GMT -8. The time now is 01:00 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.