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. [[alternative HTML version deleted]]