Question: is it possible to create this comparison?
0
gravatar for hamaor
3.2 years ago by
hamaor0
hamaor0 wrote:

i'm using deseq2 for my RNASeq analysis.

i have 2 factors, each has 2 levels:

1. genotype : col (wildtype), M6_5 (mutant)

2. treatment: Nacl, control

my design is: ~ genotype + treatment + treatment:genotype.

to get the effect of the treatment for each genotype i used:

results(dds, contrast = c("treatment","Nacl","control")

results(dds,list(c("treatment_Nacl_vs_control","genotypeM6_5.treatmentNacl"))

and to test differences between genotype on the same treatment conditions i used:

results(dds, contrast = c("genotype","M6_5","col")

results(dds, list(c("genotype_M6_5_vs_col","genotypeM6_5.treatmentNacl" ))

now, i'm looking for the comparison : M6_5 Nacl vs col control     and       M6_5 control vs col Nacl 

is that possible using my design?

 

thanks a lot

 

ADD COMMENTlink modified 3.2 years ago by Michael Love23k • written 3.2 years ago by hamaor0
Answer: is it possible to create this comparison?
0
gravatar for chimeric
3.2 years ago by
chimeric0
chimeric0 wrote:

Hi hamaor, I've found the following solution to be the most intuitive way to test whatever combination of factors and levels you're looking for.  The design from this example also looks similar to yours.

A: DESEq2 comparison with mulitple cell types under 2 conditions

Cheers,

Erin

ADD COMMENTlink written 3.2 years ago by chimeric0

hey Erin, 

it seems that it answers the pairwise comparisons of the effect of the treatment for each genotype, or the genotype gene expression on the same treatment. 

what i'm trying to do is to mix between different levels of each factor. so if i have genotype I,II and treatment A,B i'm looking for the comparison:  II A / I B   and   II B / I A. 

ADD REPLYlink written 3.2 years ago by hamaor0

Hi hamaor, I think this would still work for you--see the section of the vignette Michael referenced for more info. 

To explain, after creating the a "group" factor (dds$treatment and dds$genotype are concatenated to make 1 factor with 4 levels), you can tell the contrasts to run whatever combination of levels you prefer (colcontrol, colNaCl, M6_5control, M6_5NaCl).  In this case, your design is ~ group and you'd generate the contrasts you want by running:

results(dds, contrast=c("group","M6_5control","colNaCl"))
results(dds, contrast=c("group","M6_5NaCl","colcontrol"))
ADD REPLYlink written 3.2 years ago by chimeric0
Answer: is it possible to create this comparison?
0
gravatar for Michael Love
3.2 years ago by
Michael Love23k
United States
Michael Love23k wrote:
Take a look at the most recent vignette which goes with the current release v1.10. We show a simpler design for extracting pairwise comparisons, instead of using an interaction term. Search for "interactions"
ADD COMMENTlink written 3.2 years ago by Michael Love23k
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