Stanford University's Stephen Quake and his colleagues published a paper last month in Nature Methods in which they reported that RNA sequencing could accurately and quantitatively measure the transcriptome of single cells.
The University of California, Berkeley's Lior Pachter wrote at his blog, Bits of DNA, that the paper had a few issues. For instance, Pachter says that the experiment, like other RNA-seq studies, had a high failure rate. "The problem with the paper is that instead of reporting the failures and discarding them before analysis, they instead use all of the data when performing comparisons between single-cell and bulk RNA-Seq," Pachter writes. He adds that the authors may have then spun their results a bit too favorably.
Quake now responds at Methagora, the Nature Methods blog, that the experiments described in the paper had a 3 percent failure rate. "We conservatively included ALL of the single cell data in our analyses and thus if one follows Pachter’s prescription to only analyze the experiments that he deems 'successful,' then the results will be even better than we reported," Quake says.