Hi All, I'm trying to use DESeq for RNAseq expression analysis. I haven't been able to find information about how to deal with the following issues: 1) technical replicates We have two biological samples, two libraries (of different insert size) were prepared for each of them. so I have four lanes of data in total and I want to do differential expression between the two samples. It doesn't look quite right to me to set up the condition vector as conds <- c( "Sample1", "Sample1","Sample2","Sample2") since they are only technical replicates, not biological. But I'm not sure what to do. 2) Paired samples We have samples from three patients. For each patient, we have matched tumor and adjacent normal samples. How should we set up the analysis to capture the pair information? Thanks a lot for your help. Jinfeng