![]() |
|
![]() |
||||
Thread | Thread Starter | Forum | Replies | Last Post |
Comparing two conditions DESeq2 | rubbertjes | Bioinformatics | 4 | 03-16-2015 12:39 AM |
4 conditions in DESeq2 | mattanswers | Bioinformatics | 7 | 01-22-2015 11:15 AM |
DESeq2 (Mutant/WT + Two Conditions) | TheSeqGeek | Bioinformatics | 6 | 05-06-2014 05:04 PM |
DESeq2 glm caveats | lukas1848 | Bioinformatics | 2 | 12-06-2013 07:41 AM |
DESeq2: Difference between condition+type vs. 3 conditions | mevers | Bioinformatics | 3 | 09-02-2013 01:17 AM |
![]() |
|
Thread Tools |
![]() |
#1 | |
Junior Member
Location: UK Join Date: Jan 2015
Posts: 8
|
![]()
Hi all,
I came across this post from Simon Anders, suggesting to use a GLM if one has grouped samples across the conditions. Quote:
WT Group: INDIV1-CloneA, INDIV1-CloneB, INDIV2-CloneA, INDIV2-CloneB DISEASE Group: INDIV3-CloneA, INDIV3-CloneB, INDIV4-CloneA, INDIV4-CloneB How can I change the parameters on DESeq2 to use a GLM as Simon suggests for this type of design? |
|
![]() |
![]() |
![]() |
#2 |
Devon Ryan
Location: Freiburg, Germany Join Date: Jul 2011
Posts: 3,478
|
![]()
You'd use a design like ~INDIV+Group, where "INDIV" is 1-4 (as factors!) and "Group" is "WT" and "Disease". This assumes that there's no interaction, which you could also add in if needed.
|
![]() |
![]() |
![]() |
Tags |
bioconductor, deseq, deseq2, glm, rnaseq |
Thread Tools | |
|
|