Hello!

I am new to using compareCluster and just want to double check - the input forcompareCluster can be DESeq2 results by using both the log2fc and Entrez id: is that correct?

And one can basically just order the log2fc and Entrez id in descending order (from greatest to lowest log2fc) and extract the entire gene list?... or just the significant ones (ex: <0.05 padj) ... or does it not matter?

So, say I have 4 DESeq results/comparisons:

1. Treatment A vs. control,
2. Treatment B vs. control,
3. Treatment C vs. control
4. Treatment D vs. control

For compareCluster, I would:

1. take the DESeq results for each comparison and convert gene id/symbol to Entrez id
2. Extract entrez id and log2fc values and order them in descending order; and
3. Save as a list (I would then have, for example: GeneListA, GeneListB, GeneListC and GeneListD).

Then, I would save these 4 gene lists into a single list (e.g., myGeneList) and use it as input for compareCluster?

Clarification is much appreciated! I've been searching online for details as to what the "gene list" should look like but haven't found anything that can answer my question.

Thank you.