Question

DESEQ2 for multi-factor analysis with age(numeric), age and group

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songeric1107 • 0

@songeric1107-6996

Last seen 6.2 years ago

United States

I am trying to use DESEQ2 to estimate the correlation coefficient of gene expression levels with different phenotypes.

dds = DESeqDataSetFromMatrix(
countData = round(count),
colData = pheno1,
design = ~ Age+Gender+GROUP)

ddm <- DESeq(dds)

my questions is how could I get the coefficient for Age, gender and group, especially, age is a continuous variable

Thank you

deseq2 • 9.2k views

ADD COMMENT • link 6.2 years ago songeric1107 • 0

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Great, I got it now.

One more question, in order to get coefficient for gender and group, I have to convert them to 0,1, instead of F,M, how to interpret the coefficient of gender then?

Thank you

ADD REPLY • link 6.2 years ago songeric1107 • 0

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I moved this to a comment.

If you print the results table for sex, it will tell you the LFC direction. It’s also determined by the factor levels. See the vignette section on factor levels.

ADD REPLY • link 6.2 years ago Michael Love 43k

score 0 · Answer 1 · 2018-09-12

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Michael Love 43k

@mikelove

Last seen 4 days ago

United States

You can get the coefficients one by one with results() and the "name" argument. Or you can get all the coefficients with the coef() approach described here:

https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-to-all-calculated-values

ADD COMMENT • link 6.2 years ago Michael Love 43k