SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Using DeSeq2 with 16s data, valid parameters sarah_27_m Bioinformatics 1 01-11-2017 04:46 AM

Reply
 
Thread Tools
Old 08-22-2017, 10:36 AM   #1
aprice67
Member
 
Location: New York

Join Date: Nov 2012
Posts: 49
Question 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.

Last edited by aprice67; 08-22-2017 at 11:01 AM. Reason: Added link to sample data.
aprice67 is offline   Reply With Quote
Reply

Tags
deseq2, design, design matrix

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 09:47 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO