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Question: including information indicating upregulation/downregulation of genes in goana()
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gravatar for jhj89
2.1 years ago by
jhj8910
jhj8910 wrote:

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.

ADD COMMENTlink modified 2.1 years ago by James W. MacDonald48k • written 2.1 years ago by jhj8910
3
gravatar for James W. MacDonald
2.1 years ago by
United States
James W. MacDonald48k wrote:

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.

ADD COMMENTlink written 2.1 years ago by James W. MacDonald48k
1

The example code on the help page for goana might also help. See the example starting ## Default usage.

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Gordon Smyth35k

Dear James and Gordon,

Thank you so much! I got it to work.

ADD REPLYlink written 2.1 years ago by jhj8910
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