[BioC] Which package I should use

[Xiaoben Jiang]

Hi, I have a dataset of list name of genes and the gene hits (the number of
sequencing reads that mapped to this gene). This data set was generated by
454 sequencing data. Please see the details in my attached csv file.

The first column is the COG function category id. Column 2 -4 are 3
samples. I am interested in Sample1. I would like to find which functional
genes in Sample1 are over-representative (i.e., I'm looking for genes which
appear more often in Sample1 than those in Sample 2 and 3)

I was recommended using Bioconductor. I am a newbie in R and bioconductor.
Bioconductor include 100 packages. Can any one tell me which package can
help me do this.

Best regards,
Ben