The support.bioconductor.org editor has been updated to markdown! Please see more info at: Tutorial: Updated Support Site Editor

Question: DGE Analysis between 3 conditions
0
gravatar for evocanres
10 weeks ago by
evocanres0
evocanres0 wrote:

Hi,

I have datasets for 3 different conditions["WT", "KO", "KO1"] (each with 3 replicates). [and two time points["0" and "12"]].

To use in DESeq, I have constructed a DSElist, with design ~ group where group has 6 levels.

dds <- DESeqDataSetFromMatrix(countData = readCount,
                                 colData = readCountColData,
                                 design = ~ group)
dds <- DESeq(dds)

My objective to find genes that have higher expression in KO compared to WT and have higher expression in WT compared to KO1. This all at a single time point, lets say "0". Would it be correct if I get the difference in gene expression between KO vs WT = res1 (select log2FoldChange > 1.5) and WT vs KO = res2 (select log2FoldChange > 1.5). And then I try to find which genes in res1 have log2FoldChange higher than 1.5 compared to res2. Is this the correct way?

res1 <- results(dds, contrast = c("condition", "KO", "WT"),
                 alpha = 0.05)
res1 = na.omit(res1)
res1 = res1[res1$log2FoldChange < 1.5,]`

res2 <- results(dds, contrast = c("condition", "WT", "KO1"),
                 alpha = 0.05)
res2 = na.omit(res2)
res2 = res2[res2$log2FoldChange < 1.5,]

genelist = intersect(rownames(res1), rownames(res2)
genelist = genelist[genelist$log2FoldChange < 1.5]
rnaseq deseq2 • 82 views
ADD COMMENTlink modified 10 weeks ago by Michael Love22k • written 10 weeks ago by evocanres0
Answer: DGE Analysis between 3 conditions
0
gravatar for Michael Love
10 weeks ago by
Michael Love22k
United States
Michael Love22k wrote:

Yes I would approach this by just looking at the intersection of the two FDR sets.

ADD COMMENTlink written 10 weeks ago by Michael Love22k
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 16.09
Traffic: 454 users visited in the last hour