What is the input for clusterProfiler R pack

Question

[roy.granit]

Sorry for the very basic question, but I am new to R.

I wish to use the 'clusterProfiler' pack, but I could not understand how to format the input file for this pack.

http://www.bioconductor.org/packages/release/bioc/html/clusterProfiler.html

Looking at the 'geneList' sample file shows this format:

> head(geneList)
    4312     8318    10874    55143    55388      991 
4.572613 4.514594 4.418218 4.144075 3.876258 3.677857

Looks like gene IDs and expression values, am I correct? but how does the pack knows what are the clusters?

Thanks!

Roy

[linus]

Did you check the tutorial pdf?

They explain step by step how the analysis works.

[roy.granit]

Yes, I went trough the tutorial, it indeed details the analysis steps, but I could not find instructions on the format of the input file..

Answer 1

[Guangchuang Yu]

This question had been answer in http://guangchuangyu.github.io/2014/08/why-clusterprofiler-fails/

Bests, Guangchuang