Question: DGE Analysis between 3 conditions
0
7 months ago by
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,
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 • 141 views
modified 7 months ago by Michael Love24k • written 7 months ago by evocanres0
Answer: DGE Analysis between 3 conditions
0
7 months ago by
Michael Love24k
United States
Michael Love24k wrote:

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