Hello- It looks like you just want the counts and aren't doing a differential analysis (using edgeR and/or DESeq), is that correct? dba.report reports the result of the analsyis, with statistics measuring the confidence that the binding for each site differs. So you can;t run dba.report unless you run dba.analyze. If you want to retrieve the binding matrix with the count data for all the sites, you can do this with dba.peakset: > bindingmatrix = dba.peakset(DBA, bRetrieve=T) This returns a GRanges object — you can get it as a dataframe by setting DataType = DBA_DATA_FRAME, and also save it as a tab-delimited file (readable by Excel) by specifying a writeFile parameter: > bindingmatrix = dba.peakset(DBA, bRetrieve=T,writeFile="bindingmatrix.bed") The values in this matrix will be normalized according to what was specified in the call to dba.count. The default, DBA_SCORE_TMM_MINUS_EFFECTIVE, uses the TMM normalization from edgeR based ont he effective library size (reads in peaks), after subtracting the control reads. You can change the normalization method without having to re-count by calling dba.count with peaks=NULL, e.g.: > DBA = dba.count(DBA, peaks=NULL, score=DBA_SCORE_RPKM) > bindingmatrix.RPKM = dba.peakset(DBA, bRetrieve=T) To get the RPKM values, etc. Cheers- Rory From: 이지언 <wldsj1052@postech.ac.kr<mailto:wldsj1052@postech.ac.kr>> Date: Tue, 5 Feb 2013 01:02:39 +0900 To: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>> Subject: Question concerning Diffbind Resent-From: Rory Stark <rory.stark@cancer.org.uk<mailto:rory.stark@cancer.org.uk>> Dear Dr. Stark I am a graduate student at POSTECH and have a question concerning DiffBind. I have multiple samples of different condition but do not have any replicate nor control sample. SampleID Tissue Factor Condition Replicate K4N NA[http://mail.postech.ac.kr/t_default/ko/images/button/btn_send.gif] K4 N 1 K4H NA K4 H 1 K4C NA K4 C 1 K27N NA K27 N 1 H27H NA K27 H 1 K27C NA K27 C 1 Using DiffBind, I was able to go as far as dba.count but could not go further to dba.Report. So concerning DiffBind, I have two questions. 1. Does dba.Count give a normalized consensus matrix as described by dba,count? 2. If so, is there a way to pull the matrix out in .csv or other excel-readable format without using dba.Report? Thanks in advance Best Regards, Jieon Lee NOTICE AND DISCLAIMER This e-mail (including any attachments) is intended for the above- named person(s). If you are not the intended recipient, notify the sender immediately, delete this email from your system and do not disclose or use for any purpose. We may monitor all incoming and outgoing emails in line with current legislation. We have taken steps to ensure that this email and attachments are free from any virus, but it remains your responsibility to ensure that viruses do not adversely affect you. Cancer Research UK Registered charity in England and Wales (1089464), Scotland (SC041666) and the Isle of Man (1103) A company limited by guarantee. Registered company in England and Wales (4325234) and the Isle of Man (5713F). Registered Office Address: Angel Building, 407 St John Street, London EC1V 4AD. [[alternative HTML version deleted]]