Question

How to mention control by using contrast command in DESeq2

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Jitendra ▴ 10

@nabiyogesh-11718

Last seen 5 months ago

United Kingdom

Hi,

I have got 9 treatment (T1 to T9) and two tissue (Root and Leaf). I want to compare T1 vs rest of the treatment conditions (T2 to T9) within each tissue. I just want to know where should I put T1 in the below so that it can be used as the control for all comparison.

dds6Genus = phyloseq_to_deseq2(physeq6Genus, ~1)
dds6Genus$group <- as.factor(paste(dds6Genus$Treatment,dds6Genus$Tissue,sep="."))
design(dds6Genus) <- ~ group


dds6Genus = DESeq(dds6Genus, test="Wald", sfType = "poscounts", fitType="local")

#######################
T1.Root_vs_T2.Root<-results(dds6Genus,contrast=c("group","T1.Root","T2.Root"), cooksCutoff = FALSE)

like this rest of the comparison within each tissue
or 

T1.Root_vs_T2.Root<-results(dds6Genus,contrast=c("group","T2.Root","T1.Root"), cooksCutoff = FALSE)
which one  of these two is correct?

many thanks

DESeq2 • 656 views

ADD COMMENT • link 4.3 years ago Jitendra ▴ 10

score 0 · Answer 1 · 2020-09-03

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Michael Love 43k

@mikelove

Last seen 23 hours ago

United States

This is described in the workflow, which you might benefit from reading.

See the description of the results table here:

https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html#building-the-results-table

ADD COMMENT • link 4.3 years ago Michael Love 43k

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Thanks Michael,

I understand that I should use the contrast like this for all comparison;

T2.RootvsT1.Root<-results(dds6Genus,contrast=c("group","T2.Root","T1.Root"), cooksCutoff = FALSE) T3.RootvsT1.Root<-results(dds6Genus,contrast=c("group","T3.Root","T1.Root"), cooksCutoff = FALSE) T4.RootvsT1.Root<-results(dds6Genus,contrast=c("group","T4.Root","T1.Root"), cooksCutoff = FALSE) and like this for the comparison?

Could you please suggest if I have made any mistake to understand the contrast command?

Many thanks

ADD REPLY • link 4.3 years ago Jitendra ▴ 10

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Thanks Michael,

I understand that I should use the contrast like this for all comparison;

T2.Root_vs_T1.Root<-results(dds6Genus,contrast=c("group","T2.Root","T1.Root"), cooksCutoff = FALSE)
T3.Root_vs_T1.Root<-results(dds6Genus,contrast=c("group","T3.Root","T1.Root"), cooksCutoff = FALSE)
T4.Root_vs_T1.Root<-results(dds6Genus,contrast=c("group","T4.Root","T1.Root"), cooksCutoff = FALSE)
and like this for all the pairwise comparison?

Could you please suggest if I have made any mistake to understand the contrast command?

Many thanks

ADD REPLY • link 4.3 years ago Jitendra ▴ 10

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I don't really have time to do code review in general here, but I reserve my time for specific software questions.

ADD REPLY • link 4.3 years ago Michael Love 43k