Question: Issue with DESeq: when using DESeqDataSet object what to put under argument design when there are 3 variables
0
gravatar for catglen012
8 weeks ago by
catglen0120
catglen0120 wrote:

Hello!

My ultimate goal is for each locality, see how males and females are differentially expressed during each separate life stage.

Example: In Chicago (locality), how is my plant at the protonema stage, differentially expressed in males compared to females?

When I construct my object dds, I was wondering how can I make my dataset include only 1 locality but also include Sex, and life stages?

I am using the following so far:

dds <- DESeqDataSetFromMatrix(countData = countData, colData = colData, design = ~ Sex + Stage + Locality)

I have 3 replicates for each different locality, as well for each different sex, and life stage.

rna-seq deseq2 R • 187 views
ADD COMMENTlink modified 2 hours ago • written 8 weeks ago by catglen0120
0
gravatar for catglen012
8 weeks ago by
catglen0120
catglen0120 wrote:

Would this be a solution to this:

dds$group <- factor(paste0(dds$celltype, dds$condition))
design(dds) <- ~ group
dds <- DESeq(dds)
resultsNames(dds)
# e.g. for condition KO cell type 2 vs cell type 1
results(dds, contrast=c("group","2KO","1KO")) 
# e.g. for cell type 1 KO vs WT
results(dds, contrast=c("group","1KO","1WT"))

except instead of 2 variables it is 3? Example: dds$group <- factor(paste0(dds$celltype, dds$condition, dds$place))

ADD COMMENTlink written 8 weeks ago by catglen0120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1392 users visited in the last hour