A comparison of methods for differential expression analysis of RNA-seq data.

BACKGROUND: Finding genes that are differentially expressed between conditions is an integral part of understanding the molecular basis of phenotypic variation. In the past decades, DNA microarrays have been used extensively to quantify the abundance of mRNA corresponding to different genes, and more recently high-throughput sequencing of cDNA (RNA-seq) has emerged as a powerful competitor. As the cost of sequencing decreases, it is conceivable that the use of RNA-seq for differential expression analysis will increase rapidly. To exploit the possibilities and address the challenges posed by this relatively new type of data, a number of software packages have been developed especially for differential expression analysis of RNA-seq data. RESULTS: We conducted an extensive comparison of eleven methods for differential expression analysis of RNA-seq data. All methods are freely available within the R framework and take as input a matrix of counts, i.e. the number of reads mapping to each genomic feature of interest in each of a number of samples. We evaluate the methods based on both simulated data and real RNA-seq data. CONCLUSIONS: Very small sample sizes, which are still common in RNA-seq experiments, impose problems for all evaluated methods and any results obtained under such conditions should be interpreted with caution. For larger sample sizes, the methods combining a variance-stabilizing transformation with the 'limma' method for differential expression analysis perform well under many different conditions, as does the nonparametric SAMseq method.

The ruthenium-tin system

The Ru-Sn liquid-solid and some solid-solid equilibria have been completely revised by means of differential thermal analysis, X-ray powder diffraction and microprobe investigations. The existence of two intermetallic phases has been clearly established: Ru(0.4)Sn(0.6)decomposed by a peritectic reaction at 1266(+/-4)degrees C and Ru0.3Sn0.7 congruently melting at 1257(+/-2)degrees C.

The ruthenium-silicon system

The Ruthenium-Silicon system has been completely revised using differential thermal analysis, X-ray diffraction and electron microprobe investigations. The two equiatomic compound structures (CsCl and FeSi types) have been identified as two different phases. The occurrence of Ru,Si, was not confirmed. (C) 1999 Elsevier Science S.A. All rights reserved.