1. A method, comprising: (a) assaying by sequencing, array hybridization, or nucleic acid amplification an expression level of each of a first group of transcripts and a second group of transcripts in a fine needle aspirate test sample from a thyroid nodule of a subject, wherein said first group of transcripts includes at least two transcripts corresponding to at least two sequences selected from SEQ ID Nos. 1-2, and wherein said second group of transcripts includes at least two transcripts corresponding to at least two sequences selected from SEQ ID Nos. 7-8; and (b) in a programmed computer, comparing said expression level of each of said first group of transcripts and said second group of transcripts with reference expression levels of transcripts corresponding to sequences as set forth in SEQ ID Nos. 1-2 and 7-8 to (1) classify said thyroid nodule as malignant if there is an increase in an expression level corresponding to said first group of transcripts or a decrease in an expression level corresponding to said second group of transcripts, or (2) classify said thyroid nodule as benign if there is an increase in said expression level corresponding to said second group of transcripts or a decrease in said expression level corresponding to said first group of transcripts.