Agreement between estimated RPKM values and qRT-PCR validation for four transcript blocks in breast cell lines. We selected four transcript blocks and two transcripts for each transcript block. We compared qRT-PCR measurements and transcript expression levels estimated by several methods in the MCF7 cell line. When the corresponding method could correctly predict the direction of fold change within the HME cell line, 'o' mark is used. Otherwise, 'x' mark is used. Cufflinks*: the min-isoform-fraction parameter of Cufflinks was set to 0.0 in order to recover very low expressed transcripts. IsoformEx and Cufflinks* used the same Bowtie output files.