Identify expressed genes from combined microarray data sets
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 (edit: should be up-regulated?) 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.