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Question: Cultivar+Time+Treatment study in Deseq2
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gravatar for suren.neupane04
10 weeks ago by
SDSU
suren.neupane040 wrote:

Hi,

I am new in RNA-seq analysis via Deseq2. I want to study differential gene expression pattern in two different genotypes in two different time points with four treatments (including control) in each genotypes (3 replicates). Please suggest me the proper codes for the analyses. Models to be used: cultivar+time+cultivar:time, time+time:treatment

Thanks

# Notes:
# cultvar1= Resistance; cultivar2= Susceptible
#time1=5th day; time2=30th day
#Treatment= (4= SCN Only R; 5= Aphid Only R; 6= SCN+Aphid R, 7= COntrol R, 1= SCN Only S, 2= Aphid Only S, 3= SCN+Aphid S, 8= Control S)
cultivar <- as.factor (c(1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2))
time <- as.factor (c(1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2,2))
treatment <- as.factor (c(4,4,4,5,5,5,6,6,6,7,7,7,1,1,1,2,2,2,3,3,3,8,8,8,4,4,4,5,5,5,6,6,6,7,7,7,1,1,1,2,2,2,3,3,3,8,8,8))

cond <- data.frame(cultivar,time,treatment, stringsAsFactors=TRUE)

cond <- as.data.frame(cond)
sapply (cond, class) ##all should be factors

cond[,1] <- factor(cond[,1])
cond[,2] <- factor(cond[,2])
cond[,3] <- factor(cond[,3])
ADD COMMENTlink modified 10 weeks ago by Michael Love19k • written 10 weeks ago by suren.neupane040
0
gravatar for Michael Love
10 weeks ago by
Michael Love19k
United States
Michael Love19k wrote:

"Please suggest me the proper codes for the analyses"

This isn't exactly how the Bioconductor support site works. The goal is to provide software support, in particular beyond all of the documentation in the vignette and manual pages. You can see ?results for details on extracting contrasts after having run DESeq()

You might have a question about a particular comparison or contrast. It would be appropriate to attempt this after having read the help and examples in ?results, and then ask if this is the correct interpretation of the comparison or contrast you are interested in, but the developers do not write out all of the analysis code and its interpretation for you.

ADD COMMENTlink written 10 weeks ago by Michael Love19k
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