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


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