[BioC] error loading dba in DiffBind

[Lawson, Nathan]

Gord,

Thanks for the quick reply.

Attached is a .zip file with all of the peaksets (they are not so big since they are only from one chromosome) and the sample sheet file.

Below is session info from our cluster as well as from my computer (this is a run from the terminal, but I have also run it with the R64 GUI console with no problem).


Session info from HPCC cluster:

> sessionInfo()
R version 3.0.1 (2013-05-16)
Platform: x86_64-unknown-linux-gnu (64-bit)

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

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

other attached packages:
[1] DiffBind_1.6.2       Biobase_2.20.0       GenomicRanges_1.12.4
[4] IRanges_1.18.1       BiocGenerics_0.6.0

loaded via a namespace (and not attached):
[1] amap_0.8-7         edgeR_3.2.3        gdata_2.12.0.2     gplots_2.11.0.1
[5] gtools_2.7.1       limma_3.16.5       RColorBrewer_1.0-5 stats4_3.0.1
[9] zlibbioc_1.6.0




session info from my computer:

> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: i386-apple-darwin9.8.0/i386 (32-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
[1] DiffBind_1.4.2       Biobase_2.18.0       GenomicRanges_1.10.7
[4] IRanges_1.16.6       BiocGenerics_0.4.0

loaded via a namespace (and not attached):
 [1] amap_0.8-7         edgeR_3.0.8        gdata_2.12.0       gplots_2.11.0
 [5] gtools_2.7.1       limma_3.14.4       parallel_2.15.1    RColorBrewer_1.0-5
 [9] stats4_2.15.1      zlibbioc_1.4.0







Thanks,
Nathan

On Jun 19, 2013, at 11:24 AM, Gordon Brown <Gordon.Brown at cruk.cam.ac.uk> wrote:

> Hi, Nathan,
>
> I haven't seen messages like these.  The warnings suggest that numbers are
> being interpreted as strings, and converted to factors, but I can't
> imagine why that would happen.  Can you send along your sample sheet, and
> the first few lines of your peaks files?  I'll see if I can reproduce it.
> Also, can you let me know the sessionInfo() and operating system and
> version from both your computer and cluster?
>
> In case it helps, "dba.count" now has a "bLowMem" option that greatly
> reduces memory usage in dba.count; perhaps you will be able to get further
> on your local machine using that option.  You'll have to upgrade to R
> 3.0.1/Bioconductor 2.12 though.
>
> Cheers,
>
> - Gord
>
> On 2013-06-19 15:23, "Lawson, Nathan" <Nathan.Lawson at umassmed.edu> wrote:
>
>>
>> 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
>>
>