I'm trying to use DESeq2 to perform something like a one-way ANOVA on 3

groups of samples. I've seen the same question and answer here:

DESeq2 One-way ANOVA with 3 sample groups?

However, I can't seem to get a single p value. I have my data input successfully, and I've been able to

perform pairwise comparisons using DESeq2 but I haven't been able to

extract one p-value across 3 different groups using Mike's kind reply code in the above post. Thanks for your help.

The code I used was

group=factor(c("A","A","B","B","C","C")) design(dds) = ~ group dds = DESeq(dds, test = "LRT", reduced = ~ 1) res=results(dds)

The still give the pairwise comparison, default C vs A p values. I can use contrast to get other pairwise p values but Is there anyway I can get a single p value per gene?

>sessionInfo()

R version 3.2.1 (2015-06-18)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

locale:

[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 LC_MONETARY=English_United States.1252

[4] LC_NUMERIC=C LC_TIME=English_United States.1252

attached base packages:

[1] parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages:

[1] ggplot2_1.0.1 gplots_2.17.0 RColorBrewer_1.1-2 limma_3.24.15 BiocInstaller_1.18.4

[6] DESeq2_1.8.1 RcppArmadillo_0.5.400.2.0 Rcpp_0.12.0 GenomicRanges_1.20.6 GenomeInfoDb_1.4.2

[11] IRanges_2.2.7 S4Vectors_0.6.5 BiocGenerics_0.14.0

Thanks Mike for the prompt reply. Yes I checked and the baseMean, test stats, pvalue and padj are all the same! That makes sense. Thank you so much for your help! Our community benefit tremendously from your responses.

Hi Michael, it is easy to understand that the LRT p-value is for the comparison of the 3 levels. However, how can we retrieve the p-value for the comparison of condition B vs A?

Thank you!

You can tell results() to generate a Wald test p-value for a contrast with results(dds, ..., test="Wald"). See ?results for more.

Thanks Michael. This is exactly the answer I wanted!