Question: How does my DESeq2 code handle more than two conditions?
1
gravatar for a.rex
12 months ago by
a.rex0
a.rex0 wrote:

 

 

I am completely new to using R and DeSeq2 for RNA-seq analysis. My experimental set up is such that I have 3 biological conditions and 2 replicates per condition. I used featurescount to count transcript per genomic interval. I then plugged this into the following script: 

library(DESeq2)
countdata <- read.table("featurescountmatrix.txt", header=TRUE, row.names=1)
countdata <- countdata[ ,6:ncol(countdata)]
colnames(countdata) <- gsub(".[sb]am$", "", colnames(countdata))
countdata <- as.matrix(countdata)
(condition <- factor(c(rep("cond1", 2), rep("cond2", 2),rep("cond3", 2))))
(coldata <- data.frame(row.names=colnames(countdata), condition))
dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~condition)
dds <- DESeq(dds)
res <- results(dds,contrast=c("cond1","cond2","cond3"))
table(res$padj<0.05)
res <- res[order(res$padj), ]
resdata <- merge(as.data.frame(res), as.data.frame(counts(dds, normalized=TRUE)), by="row.names", sort=FALSE)
names(resdata)[1] <- "Gene"
head(resdata)
write.csv(resdata, file="cond123diffexpr-results.csv")

I do not understand, whether from the code above, the p-value is calculated based on the statistical difference between cond1 and cond3 or all three conditions?? 

 

 

 

deseq2 • 134 views
ADD COMMENTlink modified 12 months ago by Michael Love25k • written 12 months ago by a.rex0
Answer: How does my DESeq2 code handle more than two conditions?
0
gravatar for Michael Love
12 months ago by
Michael Love25k
United States
Michael Love25k wrote:

A good place to start is our workflow which explains what DESeq2 is testing:

https://bioconductor.org/packages/rnaseqGene

You can also read over the DESeq2 publication which helps out a lot understanding what is happening when you run the software:

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-014-0550-8

For specific functions you can look up what happens and how the different arguments work by typing ? and the function name. 

If you want to know how contrasts work in the results function type:

?results

And read about the contrast argument.

ADD COMMENTlink written 12 months ago by Michael Love25k
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