[BioC] DiffBind error loading dba.count

[Gordon Brown]

Hi, Paolo,

DiffBind uses quite a lot of memory for the dba.count step, because it loads
the whole data file into memory.  (In hindsight, not the best design
choice...)  Try running with parallelization turned off:

> test=dba.count(test,bParallel=F)

so that it only loads one file at a time, to reduce the memory footprint.
For the upcoming release, we'll probably fix this, at the cost of somewhat
slower counting.

How much RAM does your machine have?

Cheers,

 - Gord


On 2012/07/30 11:00, "Paolo Kunderfranco" <paolo.kunderfranco at gmail.com>
wrote:

> Dear All,
> I am facing some problems with RGUI loading dba.count with my dataset,
> 
>> setwd("C:/Documents and Settings/pkunderfranco/Documenti/Data/ChIP-seq
>> Roberto/Analisi_PK/DiffBind/H3K27me3/")
> 
>> library("DiffBind")
> 
>> test= dba(sampleSheet='database.csv')
> ES_H3K27 ES H3K27 1  1 raw
> CMN_H3K27 CMN H3K27 1  1 raw
> CMA_H3K27 CMA H3K27 1  1 raw
> 
>> test=dba.count(test)
> AppName: rgui.exe  AppVer: 2.150.58871.0  ModName: diffbind.dll
> ModVer: 0.0.0.0  Offset: 00003be1
> 
> Did anyone faced the same problem? which are the memory requirements
> to run DiffBind?
> Thanks,
> Paolo
> 
> 


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