Hi Robin-

The HOMER peak format is not supported natively by DiffBind. You'll need to convert the peak file format to a supported one -- the easiest is the default ("raw") which has four columns: the chromosome name, start position, end position, and the score you want to use. The key is to strip off the first column (PeakID); you should strip off the first 40 lines of header as well.

I should mention as well that with only two peaksets and no replicates, you can not really perform a meaningful differential analysis at the read count level!

Cheers-
Rory
________________________________
From: Robin Mjelle [robinmjelle@gmail.com]
Sent: 29 March 2013 11:04
To: Rory Stark; gordon@cshl.edu
Subject: Fwd: diffbind

I addition  to the previous mail I have this info:

> tcf7data
2 Samples, 19 sites in matrix (1868 total):
       ID Factor Condition Replicate Peak.caller Intervals
1 Treated  Bcell   Treated         1         raw      1480
2 Control  Bcell   Control         1         raw       407

> sessionInfo()
R version 2.15.3 (2013-03-01)
Platform: x86_64-pc-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=nb_NO.UTF-8       LC_NUMERIC=C
 [3] LC_TIME=nb_NO.UTF-8        LC_COLLATE=nb_NO.UTF-8
 [5] LC_MONETARY=nb_NO.UTF-8    LC_MESSAGES=nb_NO.UTF-8
 [7] LC_PAPER=C                 LC_NAME=C
 [9] LC_ADDRESS=C               LC_TELEPHONE=C
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods
[7] base

other attached packages:
[1] DiffBind_1.4.2       Biobase_2.18.0       GenomicRanges_1.10.7
[4] IRanges_1.16.4       BiocGenerics_0.4.0   BiocInstaller_1.8.3

loaded via a namespace (and not attached):
 [1] amap_0.8-7         edgeR_3.0.4        gdata_2.12.0
 [4] gplots_2.11.0      gtools_2.7.1       limma_3.14.1
 [7] parallel_2.15.3    RColorBrewer_1.0-5 stats4_2.15.3
[10] tools_2.15.3       zlibbioc_1.4.0












---------- Forwarded message ----------
From: Robin Mjelle <robinmjelle@gmail.com<mailto:robinmjelle@gmail.com>>
Date: Fri, Mar 29, 2013 at 11:55 AM
Subject: diffbind
To: rory.stark@cruk.cam.ac.uk<mailto:rory.stark@cruk.cam.ac.uk>


Dear Gordon or Rory,

I am trying to run DiffBind but I get an error like this (translated from norwegian):

> tcf7data <- dba.count(tcf7data)
Error in if (res[i] == -1) { :
  missing value where TRUE/FALSE is needed

I have attached my csv-input as well as my peak-file.
The peak-file is created with HOMER.


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