[BioC] error loading dba in DiffBind

[Lawson, Nathan]

I am using DiffBind to identify differentially occupied elements from histone modification ChIP-Seq between two different cell lines.

I successfully ran the package on my own computer with peaks and mapped reads limited to a single human chromosome as a test.  The analysis ran nicely and the results looked good.  Unfortunately, I was not able to run a full genome-wide analysis due to computational and space limitations.  Therefore, I tried to run the analysis on our high performance computing cluster, which is when the error appeared.

When running the SAME EXACT set of files, including the same sample sheet, on our cluster, I get the following error output, as well as additional warnings that I have not seen previously:

> AV = dba(sampleSheet="AVbothChr6.csv")
A1.0 HUAEC K27ac artery  1 raw
A1.1 HUAEC K27ac artery  2 raw
V1.0 HUVEC K27ac vein  1 raw
V1.1 HUVEC K27ac vein  2 raw
A1.2 HUAEC p300 artery  1 raw
A1.3 HUAEC p300 artery  2 raw
V1.3 HUVEC p300 vein  1 raw
V2.6 HUVEC p300 vein  2 raw
Error in if (res >= minval) { : missing value where TRUE/FALSE needed
In addition: Warning messages:
1: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
2: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
3: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
4: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
5: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
6: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
7: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
8: In Ops.factor(peaks[, pCol], width) : / not meaningful for factors
> 


Again, these datasets were successfully entered as a dba object and subsequently analyzed using DiffBind on my computer.  The original input files were simply transferred to the cluster to re-test there.  The only difference (I can see) is that the cluster is currently running R-3.0.1 and I was running 2.15.

I also tried making the peaks.bed files into a 6-column format (the original bed files only had 5 columns), but this did not seem to solve the problem.

Any suggestions are welcome.

Thanks,
Nathan

Nathan D. Lawson, Ph.D.
Associate Professor
Program in Gene Function and Expression
University of Massachusetts Medical School 
364 Plantation Street
LRB617
Worcester, MA 01605
website: lawsonlab.umassmed.edu
email: nathan.lawson at umassmed.edu
phone: 508-856-1177