Hi,

i am trying to identify tissue specific genes using deseq2. 

when i used for tissue1 vs tissue2 it works good.

but when i have 3 or more tissues, i have problem getting tissue specific genes.

ddsHTSeq <- DESeqDataSetFromHTSeqCount(sampleTable = sampleTable, directory = directory, design= ~ condition)

ddsHTSeq <- ddsHTSeq[ rowSums(counts(ddsHTSeq)) > 1, ]

de=DESeq(ddsHTSeq, betaPrior = TRUE)

c14G <- results(de, name="condition14G")

c16G <- results(de, name="condition16G")

c32G <- results(de, name="condition32G")

##alternatively i also tried 

c14Gc <-  results(de, contrast = list(c("condition14G"), c("condition16G","condition32G")))

c16Gc <-  results(de, contrast = list(c("condition16G"), c("condition14G","condition32G")))

c32Gc <-  results(de, contrast = list(c("condition32G"), c("condition16G","condition14G")))

## both name and contrast gives almost same results,  some genes showed up in two tissues, but i want only tissue specific genes,

for example 'gene1' upregulated in condition14G and condition16G compare to condition32G, but this gene showed up as tissue specific genes in both the lists c14Gc and c16Gc. i dont want genes with this type in my list.

'gene6' expressed or unregulated only in condition16G compare to two other condition14G and condition32G, this should be tissue specific gene for condition16G

I am new to this, unable to extract tissue specific genes. It will be great help if any one suggest how to filter the tissue specific genes.

Thank you

Madhu

If by tissue specific, you mean that its expression level is different in tissue X compared to all others, you would have to perform all the pairwise tests and take the intersection of the DE gene lists.