Is this DESeq2 interactions design correct?
1
0
Entering edit mode
bhagyesh • 0
@2f7cb167
Last seen 5 days ago
United States

I am running a cell-based screen by introducing a library of mutants into a reporter cell line and then sorting them via FACS. I have two conditions--control and treatment and cells from each condition are sorted into "top" and "bottom" pools based on the reporter activity. I have triplicates for each condition so 12 samples in total. Now I want to compare the difference in the ratio of top/bottom between the two conditions. Since top and bottom pools are derived from the same cell population for each replicate, I thought of adding a batch interaction term for pair-wise comparison.

coldata <- data.frame(
  c("sample1", "sample2", "sample3","sample4","sample5","sample6",
    "sample7", "sample8", "sample9","sample10","sample11","sample12"),
  batch = rep(c("1","2","3"),3),
  sort=rep(c("top","bottom"),6),
  condition=c(rep("control",6), rep("treatment",6))

  dds <- DESeqDataSetFromMatrix(countData = E,
                              colData = coldata,
                              design = ~ batch + sort + condition + sort:condition)

dds$condition <- relevel(dds$condition, ref="control")
dds$sort <- relevel(dds$sort, ref="bottom")

dds <- DESeq(dds)
resultsNames(dds)

The resultNames returns

[1] "Intercept" "batch_2_vs_1" "batch_3_vs_1" "sort_top_vs_bottom"
[5] "condition_treatment_vs_control" "sorttop.conditiontreatment"

Is my design correct and if so is sorttop.conditiontreatment what I am ultimately looking for?

DESeq2 interactions • 124 views
ADD COMMENT
0
Entering edit mode
@mikelove
Last seen 5 hours ago
United States

Check the vignette section on interactions. If you need further guidance on how to interpret results columns, I'd recommend consulting with a local statistician or someone familiar with linear models in R.

ADD COMMENT

Login before adding your answer.

Traffic: 356 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6