A method of detecting an individual cell of a specified type in a sample comprising a mixture of cell types, which mixture comprises at least one cell of the specified type, wherein the cell comprises a first nucleic acid target and a second nucleic acid target, wherein the first and second nucleic acid targets always co-exist in the cell, the method comprising: (a) providing a first label probe comprising a first label, and providing a second label probe comprising a second label, wherein a first signal from the first label is indistinguishable from a second signal from the second label; (b) capturing, in the cell, the first label probe to the first nucleic acid target, when present in the cell, and the second label probe to the second nucleic acid target, when present in the cell, wherein the first and second nucleic acid targets are separate molecules, wherein the capturing comprises: providing for the first nucleic acid target at least a first capture probe and providing for the second nucleic acid target at least a second capture probe; capturing the first label probe to the first nucleic acid target, comprising hybridizing in the cell the first capture probe to the first target nucleic acid, and hybridizing the first label probe to the first capture probe, thereby capturing the first label probe to the first nucleic acid target; and capturing the second label probe to the second nucleic acid target, comprising hybridizing in the cell the second capture probe to the second target nucleic acid, and hybridizing the second label probe to the second capture probe, thereby capturing the second label probe to the second nucleic acid target; (c) detecting the signal from the labels; (d) correlating the signal detected from the cell with the presence or amount of the first and second nucleic acid targets in the cell; and (e) identifying the cell as being of the specified type based on detection of the presence or amount of the first and second nucleic acid targets within the cell, wherein the specified type of cell is distinguishable from the other cell type(s) in the mixture on the basis of either the presence or amount of the first nucleic acid target and the presence or amount of the second nucleic acid target in the cell. (a) providing a first label probe comprising a first label, and providing a second label probe comprising a second label, wherein a first signal from the first label is indistinguishable from a second signal from the second label; (b) capturing, in the cell, the first label probe to the first nucleic acid target, when present in the cell, and the second label probe to the second nucleic acid target, when present in the cell, wherein the first and second nucleic acid targets are separate molecules, wherein the capturing comprises: providing for the first nucleic acid target at least a first capture probe and providing for the second nucleic acid target at least a second capture probe; capturing the first label probe to the first nucleic acid target, comprising hybridizing in the cell the first capture probe to the first target nucleic acid, and hybridizing the first label probe to the first capture probe, thereby capturing the first label probe to the first nucleic acid target; and capturing the second label probe to the second nucleic acid target, comprising hybridizing in the cell the second capture probe to the second target nucleic acid, and hybridizing the second label probe to the second capture probe, thereby capturing the second label probe to the second nucleic acid target; providing for the first nucleic acid target at least a first capture probe and providing for the second nucleic acid target at least a second capture probe; capturing the first label probe to the first nucleic acid target, comprising hybridizing in the cell the first capture probe to the first target nucleic acid, and hybridizing the first label probe to the first capture probe, thereby capturing the first label probe to the first nucleic acid target; and capturing the second label probe to the second nucleic acid target, comprising hybridizing in the cell the second capture probe to the second target nucleic acid, and hybridizing the second label probe to the second capture probe, thereby capturing the second label probe to the second nucleic acid target; (c) detecting the signal from the labels; (d) correlating the signal detected from the cell with the presence or amount of the first and second nucleic acid targets in the cell; and (e) identifying the cell as being of the specified type based on detection of the presence or amount of the first and second nucleic acid targets within the cell, wherein the specified type of cell is distinguishable from the other cell type(s) in the mixture on the basis of either the presence or amount of the first nucleic acid target and the presence or amount of the second nucleic acid target in the cell.