Question: DESeq2 correct pairwise comparisions
gravatar for hamsasekar02
22 months ago by
hamsasekar020 wrote:

I have resultNames(dds) as -: Model -

dds <- DESeqDataSetFromMatrix( + countData = countTable, + colData = colTable, design = ~ condition+time+condition:time)

dds_lrt_time <- DESeq(dds, test="LRT", reduced = ~ condition + time)

resultsNames(dds_lrt_time) [1] "Intercept" "condition_infected_vs_mock" [3] "time_4dpi_vs_2dpi" "conditioninfected.time4dpi"

For a genotype I want to compare 4 dpi vs 2dpi in mock vs infected levels.

I have used "condition_infected_vs_mock" for DGEs for mock vs infected levels at 2dpi

"condition_infected_vs_mock","conditioninfected.time4dpi" for DGEs at mock vs infected levels at 4dpi

But now I want to compare infected vs mock levels at time 4dpi vs 2dpi Can i use this interaction term "conditioninfected.time4dpi" for this comparision.

rna-seq • 1.1k views
ADD COMMENTlink modified 22 months ago • written 22 months ago by hamsasekar020
gravatar for Kevin Blighe
17 months ago by
Kevin Blighe69k
Republic of Ireland
Kevin Blighe69k wrote:

Please take a look at my answer, here: A: DESeq2 compare all levels

ADD COMMENTlink modified 6 months ago • written 17 months ago by Kevin Blighe69k
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