Dear all, I would like to enquire about the DESeq package. My student and I have been using the package to analyse our microbial RNA-Seq data, which we obtained from oral clinical samples. Following the steps described in the "Differential expression of RNA- Seq data at the gene level - the DESEq package" and using 2 different computers (a MacBook air and a Windows 7 PC) on the same data, we seem to have obtained different outputs for the normalized mean values vs log2 fold change. See attached. Please can you help us understand why we get different outputs? Thank you Kind regards Thuy

Hi On 16/07/14 17:25, Thuy Do wrote: > I would like to enquire about the DESeq package. My student and I have been using the package to analyse our microbial RNA-Seq data, which we obtained from oral clinical samples. > Following the steps described in the "Differential expression of RNA-Seq data at the gene level - the DESEq package" and using 2 different computers (a MacBook air and a Windows 7 PC) on the same data, we seem to have obtained different outputs for the normalized mean values vs log2 fold change. See attached. > Please can you help us understand why we get different outputs? are you sure you have the same version of DESeq on both machines? Use the "sessionInfo()" command to check. Also, if you are just staring, please consider using DESeq2. The old DESeq package is quite outdated methodology by now. Simon