Question: JunctionSeq pairwise contrast with a multi-level treatment
0
gravatar for stuart
2.9 years ago by
stuart0
stuart0 wrote:

Hi,

Does anyone know how to contrast only a single pair of conditions in JunctionSeq (which is based on DEXseq AFAIK), if there are > 2 levels of the condition? I would like to test the null hypothesis that there is no condition:bin effect between one pair of conditions, but still using information from the untested conditions to better estimate the dispersion.

For example, in the JunctionSeq manual pg 40 they give code for testing a single, 3-level condition in the example data:

threeLevelVariable <- c("GroupA","GroupA",
"GroupB","GroupB",
"GroupC","GroupC");

jscs <- runJunctionSeqAnalyses(sample.files = countFiles,
sample.names = decoder$sample.ID,
condition=factor(threeLevelVariable),
flat.gff.file = gff.file,
nCores = 1,
analysis.type = "junctionsAndExons"
);

How could I request a Group A vs Group B contrast, without throwing away the information on dispersion contained in the data for Group C?

Thank you

 

ADD COMMENTlink written 2.9 years ago by stuart0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 260 users visited in the last hour