Dear listers, I have SOLiD Small-RNA Seq data for 250 samples, which are divided into three sample types: 1 (n=50), 2 (n=100) and 3 (n=100). I have a couple of doubts regarding how to proceed with the differential expression analysis: 1) I want to compute differential expression analysis between each pair of sample types (1 vs. 2, 1 vs. 3, 2 vs. 3). Do I need to estimate the dispersions of each miRNA for each comparison (using only the two sample types of interest in that comparison)? Or is it better to estimate the dispersion only once using the three sample types together and then compute the differential expression using this overall dispersion? 2) When comparing types 2 vs. 3, I have a paired experimental design (sample 1 from type 2 is the same as sample 1 from type 3). I would like to use this information to get more power in my analysis. Is it possible to perform a paired analysis with DESeq? Thank you very much in advance for your help! Best, Xavi. ------ Xavier Solé Acha, PhD Unitat de Biomarcadors i Susceptibilitat Unit of Biomarkers and Susceptibility Institut Català d'Oncologia // Catalan Institute of Oncology Av. Gran Via de L'Hospitalet 199-203 08908 L'Hospitalet de Llobregat, Barcelona, Spain. Phone: +34 93 260 71 22 / +34 93 260 71 86 (ext. 7122) Fax: +34 93 260 71 88 E-mail: x.sole (at) iconcologia.net [[alternative HTML version deleted]]