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Question: DESEQ2 for multi-factor analysis with age(numeric), age and group
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gravatar for songeric1107
9 weeks ago by
United States
songeric11070 wrote:

 

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

ADD COMMENTlink modified 9 weeks ago • written 9 weeks ago by songeric11070

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 REPLYlink written 9 weeks ago by songeric11070

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 REPLYlink written 9 weeks ago by Michael Love20k
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gravatar for Michael Love
9 weeks ago by
Michael Love20k
United States
Michael Love20k wrote:

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 COMMENTlink modified 9 weeks ago • written 9 weeks ago by Michael Love20k
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