I have previously used DESeq to analyse differential binding in ChIP- seq data (2 replicates of two ChIP samples). I believe the newer versions of DESeq (i have 1.6.1) are able to consider the matching input samples to correct for the background reads. Does anyone have experience of including the background (input) reads in a DESeq analysis? I am afraid i am not sure how to proceed using the vignette. Is there are ChIP-seq workflow anywhere? Thanks! Ian [[alternative HTML version deleted]]

Hi, Ian, You might consider using DiffBind, which wraps DESeq (and EdgeR) into a set of tools designed for ChIP differential binding. The vignette includes some examples of differential binding analyses. The use of replicates and input or background samples is included. It's part of Bioconductor 2.9, in R 2.14.x. Cheers, - Gord On 2012/01/31 16:46, "Ian Donaldson" <ian.donaldson at="" manchester.ac.uk=""> wrote: > I have previously used DESeq to analyse differential binding in ChIP-seq data > (2 replicates of two ChIP samples). I believe the newer versions of DESeq (i > have 1.6.1) are able to consider the matching input samples to correct for the > background reads. > > Does anyone have experience of including the background (input) reads in a > DESeq analysis? I am afraid i am not sure how to proceed using the vignette. > Is there are ChIP-seq workflow anywhere? > > Thanks! > Ian > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for ...{{dropped:16}}