Hi,

To put it simply, I have a list of genes with information about whether they are upregulated or downregulated. What should the format of the input be when using goana() such that I can include the information about upregulation or downregulation of each of the genes? I understand that goana() can accept a vector of genes or MArrayLM fit object.

Thank you.

It's not necessarily clear from the help for goana, but there's this:

Arguments:

      de: a vector of Entrez Gene IDs, or a list of such vectors, or an
          'MArrayLM' fit object.

And the trick is the 'a list of such vectors' part, which is what is extracted if you feed goana an MArrayLM object. So if you do

deGenes <- list(Up = <vector of up-regulated Entrez Gene IDs>, Down = <vector of down-regulated Entrez Gene IDs>)

result <- goana(deGenes, universe = <universe of Entrez Gene IDs from your experiment>, <other arguments go here>)

Then you will get tests for up and down regulated genes.