I've had a look and, at least for these three peak files, the sample sheet works (I can not reporduce the problem).

What is very unusual is that the call to dba seems to be returning nothing, without any errors or even warnings. So the first thing to to figure out what is being returned. After you call dba:

> setwd(system.file("extra", package="DiffBind"))
> tamoxifen=dba(sampleSheet="tamoxifen.csv",peakFormat="bed")
Try seeing what "tamoxifen" has been set to:
> tamoxifen
> class(tamoxifen)
before proceeding.

You can also play with the full tamoxifen example in the vignette, including the peaks and reads. Here is a link:

https://www.dropbox.com/s/bqxnqhvr7sol1za/DiffBindVignette.zip

If you unzip this and make it your working directory, you should be able to run all the steps, and you can substitute in your peaks (and ultimately reads).

Let me know what is being returned, I'm quite curious now!

-Rory


From: $B9bJ8D6(B-$BCf;3Bg3X(B <gwc19880401@163.com<mailto:gwc19880401@163.com>>
Date: Tue, 11 Mar 2014 23:22:23 +0800
To: Rory Stark <rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>>
Subject: RE: data process before overlap analysis with the DiffBind

Thanks a lot.
At 2014-03-11 23:12:02,"Rory Stark" <Rory.Stark@cruk.cam.ac.uk<mailto:Rory.Stark@cruk.cam.ac.uk>> wrote:
OK, this should be a stable version.

Can you send me a copy of your sample sheet, and one or ore of the peak (bed) files?

-Rory
________________________________
From: $B9bJ8D6(B-$BCf;3Bg3X(B [gwc19880401@163.com<mailto:gwc19880401@163.com>]
Sent: 11 March 2014 15:03
To: Rory Stark
Subject: RE: data process before overlap analysis with the DiffBind

Dear Stark,
So appreciating  for  your quick reply and my version is:
R version 3.0.2 (2013-09-25)    DiffBind_1.8.4       GenomicRanges_1.14.4 XVector_0.2.0        IRanges_1.20.7       BiocGenerics_0.8.0  amap_0.8-12        bitops_1.0-6       caTools_1.16       edgeR_3.4.2        gdata_2.13.2       gplots_2.12.1      gtools_3.3.1       KernSmooth_2.23-10
 limma_3.18.13      RColorBrewer_1.0-5 stats4_3.0.2       tools_3.0.2        zlibbioc_1.8.0

At 2014-03-11 19:42:42,"Rory Stark" <Rory.Stark@cruk.cam.ac.uk<mailto:Rory.Stark@cruk.cam.ac.uk>> wrote:
Hello-

Can you tell me exactly what version of DiffBind you are using? (you get get this from sessionInfo()). The recent development versions may be unstable (especially DiffBind 1.9.10). Then we can get to the bottom of this matter!

Cheers-
Rory

________________________________
From: $B9bJ8D6(B-$BCf;3Bg3X(B [gwc19880401@163.com<mailto:gwc19880401@163.com>]
Sent: 11 March 2014 10:39
To: Rory Stark
Subject: data process before overlap analysis with the DiffBind

Dear Stark,
The DiffBind package is now widely used for chip data analysis owing to your ingenious design. When I utilize this package to analyze the overlap of my data from GEO, I have some trobles.
> bedfilelist=dba(sampleSheet="bedfilelist.csv",peakFormat="bed")
> bedoverlap=dba.overlap(bedfilelist,mode=DBA_OLAP_PEAK)
Error in pv.check(DBA) : object 'bedfilelist' not found
I am sure that the files are in the correct directory and the format of the
"bedfilelist.csv" is the same as the "tamoxifen.csv" as well as the raw data(except in my raw bed file, there are five columns). I then load the raw bed data provided in the package.
>tamoxifen=dba(sampleSheet="tamoxifen.csv",peakFormat="bed")
> tamoxifen=dba.overlap(tamoxifen,mode=DBA_OLAP_PEAK)
Error in pv.check(DBA) : object 'tamoxifen' not found
The situation seemed the same. But When I used the code:
>data(tamoxifen_peaks)
> tamoxifen=dba.overlap(tamoxifen,mode=DBA_OLAP_RATE)
It works. I used the function "attributes" to figure out the structure of "tamoxifen" derived from the "data(tamoxifen_peak)" and found that:
> attributes(tamoxifen)
$names
 [1] "config"      "chrmap"      "peaks"       "class"       "masks"       "samples"     "allvectors"  "overlapping" "vectors"     "attributes"  "minOverlap"
$class
[1] "DBA"
So, my question is that how to construct a the "tamoxifen" derived from the "data(tamoxifen_peak)" with the raw bed file and sampleSheet?

Thank you very much and with my best wishes to you and your family~_~
Yours,
Wenchao, Gao
Sun Yat-sen University, guangzhou, China








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