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Question: Phyloseq to DESeq2
gravatar for staffordvigors
26 days ago by
staffordvigors0 wrote:

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.


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

phyloseq deseq2 • 62 views
ADD COMMENTlink modified 26 days ago by Michael Love21k • written 26 days ago by staffordvigors0
Answer: Phyloseq to DESeq2
gravatar for Michael Love
26 days ago by
Michael Love21k
United States
Michael Love21k wrote:

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.

ADD COMMENTlink written 26 days ago by Michael Love21k

Hi Micheal,

That's fantastic, that really clears it up.

Kind regards,


ADD REPLYlink written 25 days ago by staffordvigors0
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