Hey there,

I am having an issue with phyloseq to deseq. I have looked at the vignette and the other examples to this but I still cant figure it out.

I am trying to look at the interaction between two factors. The two factors are named Group and RFI. The dataset is listed below. I tried the phyloseq to deseq code which is below.

diagdds = phyloseqtodeseq2(kostic, ~ RFI + Group + RFI*Group)

This seems to work fine for the individual factors, but is wrong for the interaction I think. This is the output. I want the interaction to be run between RFI*Group but it seems to be taking a subset (LRFI & B) rather than the complete dataset.

resultsNames(diagdds) [1] "Intercept" "RFILRFIvsHRFI" "GroupBvsA" "RFILRFI.GroupB"

Any help would be greatly appreciated.

Stafford

SampleID Group RFI Sample14 A LRFI Sample15 A HRFI Sample16 A LRFI Sample17 A HRFI Sample18 A LRFI Sample19 A HRFI Sample20 A LRFI Sample21 A HRFI Sample22 A LRFI Sample23 A HRFI Sample24 A LRFI Sample25 A HRFI Sample26 A LRFI Sample27 A HRFI Sample28 A LRFI Sample29 A HRFI Sample54 B LRFI Sample55 B HRFI Sample56 B HRFI Sample57 B HRFI Sample58 B LRFI Sample59 B HRFI Sample60 B LRFI Sample61 B HRFI Sample62 B LRFI Sample63 B LRFI Sample64 B LRFI Sample65 B LRFI Sample66 B LRFI Sample67 B LRFI Sample68 B HRFI Sample69 B LRFI Sample70 B HRFI Sample71 B HRFI Sample72 B HRFI Sample73 B HRFI Sample74 B LRFI Sample75 B HRFI Sample76 B HRFI Sample77 B LRFI

This is how R names interaction terms. If we have covariates X and Y, the interaction means there is an additional term when X=1 and Y=1. So R calls the interaction term X1.Y1. You can see this in the examples in ?results and in the vignette section on interactions.