51 views DESeq2 RNAseq differential expression analysis
1
0
Entering edit mode
adeler001 • 0
@adeler001-21743
Last seen 8 months ago
Canada

Hello Im trying to do an RNA seq differential expression analysis using DESeq2 by doing a likelihood ratio test The DESeq2 manual states " The likelihood ratio test can be performed by ...providing a reduced design formula, e.g. one in which a number of terms from design(dds) are removed"

They then shows this as an example script you would use to this : dds <- DESeq(dds, test="LRT", reduced=~1)

1) how do you determine how many terms are removed from design(dds) ? 2) Is the number of terms removed always 1 like they show in the example script above ?

deseq2 likelihood ratio rna seq wald test • 278 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 23 hours ago
United States

You can remove as many coefficients as you want. This is up to you as the analyst.

You can either provide a reduced design formula, as above, or you can provide model matrices directly:

dds <- DESeq(dds, test="LRT", full=mm, reduced=mm0)

Where mm and mm0 are created by model.matrix().

ADD COMMENT

Login before adding your answer.

Traffic: 265 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6