DESEQ2 Time Course Data

Question

[tirza.doniger]

I have time-series data - 4 time points - each has 9 replicates. I used the LRT in DESEQ2 to analyze the data. But it only compares all the time points to time zero. How can I compare all vs all time-points?

Thanks!

Tirza

ddsLRT <- DESeqDataSetFromMatrix(countData = merged_counts,
                                 colData = colData,
                                 design= ~ref + Quarter)


ddsLRT <- estimateSizeFactors(ddsLRT)
ddsLRT <- estimateDispersions(ddsLRT)
ddsLRT <- nbinomLRT(ddsLRT, reduced = ~ ref)
resLRT <- results(ddsLRT)
table(resLRT$padj < 0.1)

resultsNames(ddsLRT)

[tirza.doniger]

Thanks! That works. But how come these contrasts don't appear in the resultNames(ddsLRT)?

What if I want one condition vs multiple other conditions?

[Kevin Blighe]

But how come these contrasts don't appear in the resultNames(ddsLRT)?

They do not have to be mentioned there.

There is more information via ?results

contrast: this argument specifies what comparison to extract from the
          ‘object’ to build a results table. one of either:

            • a character vector with exactly three elements: the name
              of a factor in the design formula, the name of the
              numerator level for the fold change, and the name of the
              denominator level for the fold change (simplest case)

            • a list of 2 character vectors: the names of the fold
              changes for the numerator, and the names of the fold
              changes for the denominator. these names should be
              elements of ‘resultsNames(object)’. if the list is length
              1, a second element is added which is the empty character
              vector, ‘character()’. (more general case, can be to
              combine interaction terms and main effects)

            • a numeric contrast vector with one element for each
              element in ‘resultsNames(object)’ (most general case)

          If specified, the ‘name’ argument is ignored.

    name: the name of the individual effect (coefficient) for building
          a results table. Use this argument rather than ‘contrast’ for
          continuous variables, individual effects or for individual
          interaction terms. The value provided to ‘name’ must be an
          element of ‘resultsNames(object)’.

Then also check the examples given at the end of the output of ?results.

If you cannot find there what you need, then please consider creating a new variable that would permit you to achieve the desired contrasts.

Answer 1

[ATpoint]

Please read about contrasts: http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#contrasts