Question: DESeq2 correct pairwise comparisions
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gravatar for hamsasekar02
10 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 • 539 views
ADD COMMENTlink modified 10 months ago • written 10 months ago by hamsasekar020

These types of questions relating to DESeq2 model formulae are among the most common that are asked. Have you not searched for an answer to your question before coming here? To obtain a quicker response and from the developer of DESeq2, I suggest that you post this at Bioconductor: https://support.bioconductor.org/t/Latest/ When you post on Bioconductor, please let them know that you have also posted here.

ADD REPLYlink modified 10 months ago • written 10 months ago by Kevin Blighe54k

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

ADD REPLYlink written 5 months ago by Kevin Blighe54k
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