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What is the input for clusterProfiler R pack

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

clusterprofiler r input
• 10,806 views • link
updated by Ram Ram • written by roy.granit roy.granit

Did you check the tutorial pdf?

They explain step by step how the analysis works.

• 1 views • link
updated by Ram Ram • written by linus linus

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..

• 0 views • link
updated by Ram Ram • written by roy.granit roy.granit

1 answer

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

Bests, Guangchuang

• 1 views • link
updated by Ram Ram • written by Guangchuang Yu Guangchuang Yu

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