[BioC] Could you help us about DiffBind

賴勇志 d92b41001 at ntu.edu.tw
Thu Jun 5 19:49:48 CEST 2014

Hi Rory,

Thanks you so much. I will try what you suggest.


From: Rory Stark
Sent: Thursday, June 05, 2014 3:49 AM
To: 賴勇志
Cc: Gordon Brown ; bioconductor at r-project.org
Subject: Re: Could you help us about DiffBind

Hi Gary-

The plot should appear in the lower-left pane, which has tabs for Files,
Plots, Packages, etc. I see in the screenshot that the pane is there and
set to Plots, but it may be too small to show the plot -- you can try
making the console pane smaller to enlarge the plot pane.

I also see that you are using a somewhat dated version of R and hence of
the DiffBind (and all other Bioconductor) packages. If possible, you may
want to try updating to the most recent released version of R (v. 3.1.0)
and reloading Bioconductor 2.14.


On 04/06/2014 19:39, "賴勇志" <d92b41001 at ntu.edu.tw> wrote:

>Hi Gordon,
>Thank you so much. Based on your suggestion, I can successfully input my
>data as in the attached fig1. However, after typing
>dba.plotHeatmap(feather), there is only a matrix, but no heat map graph
>(fig2). I am sorry, this is the first time I perform R, could you teach
>how to get a heat map figure? Many thanks.
>From: Gordon Brown
>Sent: Wednesday, June 04, 2014 1:13 AM
>To: 賴勇志
>Cc: Rory Stark
>Subject: Re: Could yo help us about DiffBind error
>Hi, Gary,
>Try telling DiffBind what the peak format is, like so:
>> feather = dba (sampleSheet="feather.csv",peakFormat="bed")
>The default format (if I recall correctly) is "raw", not "bed".
>Hope this helps,
>- Gord
>From:  賴勇志 <d92b41001 at ntu.edu.tw>
>Date:  Tuesday, 3 June 2014 19:25
>To:  Rory Stark <Rory.Stark at cruk.cam.ac.uk>, Gord Brown
><gordon.brown at cruk.cam.ac.uk>
>Subject:  Could yo help us about DiffBind error
>>Dear Rory and Gordon,
>>I would like to use the DiffBind to analyze our ChIP-Seq data. I can run
>>tamoxifen example in RStudio (fig1, the
>> right side). However, when I run our own data, there are some errors as
>>the below and the left side of fig1. The attached are two .bed files of
>>our samples peak called by MACS (the fifth column is the enrichment fold
>>change) and our sample sheet. Could you
>> help us to solve this problem? Many thanks.
>>> feather = dba (sampleSheet="feather.csv")
>>FE7_K27ac_PW25 Feather H3K27ac E7
>>1 raw
>>FE7_K27ac_PW51 Feather H3K27ac E7
>>2 raw
>>>>Error in if (res >= minval) { : missing value where TRUE/FALSE needed
>>> warnings()
>>Warning messages:
>>1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
>>2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors

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