blah.js

var NUM_BINS = 2;

var data = [
	[5, 15, 25, 35],
	[25, 35, 5, 15],
	[25, 25, 15, 5],
	[0, 10, 20, 40]
]

var all = Array.prototype.concat.apply([], data)

var bins = d3.scale.linear().domain([d3.min(all), d3.max(all)]).ticks(NUM_BINS);

var numCells = data[0].length;

var genesByBin = bins.reduce(function (acc, bin, binIdx) {acc[binIdx] = []; return acc}, {});
var binsByGene = data.reduce(function (acc, gene, geneIdx) {acc[geneIdx] = []; return acc}, {});

for (var cellIdx = 0; cellIdx < numCells; cellIdx++) {
  var cell = data
	.map(function (gene, geneIdx) {	return {geneIdx: geneIdx, rpkm: gene[cellIdx]} } )
	.sort(function (a, b) { return a.rpkm - b.rpkm })
  
  var binIdx = 0;
  var binLength = bins.length;
  
  cell.forEach(function (gene) {
	while (true) {
		if (gene.rpkm <= bins[binIdx + 1]) {
			genesByBin[binIdx].push(gene.geneIdx);
			binsByGene[gene.geneIdx].push(binIdx);
			break;
		}
		binIdx += 1;
		if (binIdx >= binLength) throw new Error("Couldn't place all elements in bins.");
	}
  });
}

for (var cellIdx = 0; cellIdx < numCells; cellIdx++) {
}