Hi all,

I have a dataset consisted of 11 cell types with each cell type having >=5
replicates. For my biological question, I need to identify the unregulated
genes of each cell type and the genes do not have to be differentially
expressed compared to all the others or cell type specific.

(1) I ranked all the genes within each array and would like to identify the
genes that are consistently ranked in the top 50% of all the genes. What
statistical methods that I shall use? How about estimating FDR?
(2) To complement gene list from (1), I also need to find genes that are
consistently ranked higher in the interested cell type than in all the
other cell types, but these genes are not necessarily ranked within the top
50% of all the genes. What statistical methods that I shall use for this
purpose?

Is there a BioConductor package to achieve these two goals.

Thank you very much. Any advice is much appreciated.

Wendy

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