Question: DGE Analysis between 3 conditions
0
gravatar for prabin.dm
8 months ago by
prabin.dm160
USA/Amherst/Umass
prabin.dm160 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]

Thank you in advance

edger rna-seq deseq • 358 views
ADD COMMENTlink modified 8 months ago • written 8 months ago by prabin.dm160
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: 1075 users visited in the last hour