Hi Bioconductor Developers and Users,

I'm using Minfi package 1.8.9 to analyze .IDAT files of Illumina 450k chip.

I've implemented my pipeline to process data and to execute custom filters
and so my goal now is focused to obtain DMRs by bumphunter-methods
seen that minfi package interfaces with bumphunter package.

When I start the bumphunter method with the reccomended parameters by the
reference manual (B=1000 and parallelized process with other package like
doParallel),
the system has a performance decrease making it necessary to kill process
and reboot the system if the parallelism is to all ncores or the bumphunter
method hangs without producing results.

Is there an estimation of the execution time for results relating DMRs?
Is there an estimation of the storage space (temp and caching included)?
Is to large the dataset (also if first I considered all 12 samples then I
reduced the number to 4 samples)?
Would it be better to parallelize only on some of the ncores?


***** Output and sessionInfo *****

class: GenomicRatioSet
dim: 473462 4
exptData(0):
assays(3): Beta M CN
rownames(473462): cg13869341 cg14008030 ... cg07660283
  cg09226288
rowData metadata column names(0):
colnames(4): 9344737133_R03C01 9344737133_R01C02
  9344737133_R04C01 9344737133_R02C02
colData names(9): Sample_Name Sample_Well ... Basename filenames
Annotation
  array: IlluminaHumanMethylation450k
  annotation: ilmn12.hg19
Preprocessing
  Method: SWAN (based on a MethylSet preprocesses as 'Raw (no normalization
or bg correction)'
  minfi version: 1.8.9
  Manifest version: 0.4.0


[bumphunterEngine] Computing coefficients.
[bumphunterEngine] Performing 1000 permutations.
[bumphunterEngine] Computing marginal permutation p-values.
[bumphunterEngine] cutoff: 0.05
[bumphunterEngine] Finding regions.






[bumphunterEngine] Found 273952 bumps.
[bumphunterEngine] Computing regions for each permutation.
Loading required package: rngtools
Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

The following object is masked from 'package:IRanges':

    new2

[bumphunterEngine] Estimating p-values and FWER.


> sessionInfo()
R version 3.0.2 (2013-09-25)
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=en_US.UTF-8       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] doParallel_1.0.6     doRNG_1.5.5          rngtools_1.2.3
 [4] pkgmaker_0.17.4      registry_0.2         minfi_1.8.9
 [7] bumphunter_1.2.0     locfit_1.5-9.1       iterators_1.0.6
[10] foreach_1.4.1        Biostrings_2.30.1    GenomicRanges_1.14.4
[13] XVector_0.2.0        IRanges_1.20.6
reshape_0.8.4
[16] plyr_1.8             lattice_0.20-24      Biobase_2.22.0
[19] BiocGenerics_0.8.0

loaded via a namespace (and not attached):
 [1] annotate_1.40.0       AnnotationDbi_1.24.0  base64_1.1
 [4] beanplot_1.1          codetools_0.2-8       compiler_3.0.2
 [7] DBI_0.2-7             digest_0.6.4          genefilter_1.44.0
[10] grid_3.0.2            illuminaio_0.4.0      itertools_0.1-1
[13] limma_3.18.11         MASS_7.3-29           matrixStats_0.8.14
[16] mclust_4.2            multtest_2.18.0       nlme_3.1-113
[19] nor1mix_1.1-4         preprocessCore_1.24.0 RColorBrewer_1.0-5
[22] R.methodsS3_1.6.1     RSQLite_0.11.4        siggenes_1.36.0
[25] splines_3.0.2         stats4_3.0.2          stringr_0.6.2
[28] survival_2.37-7       tools_3.0.2           XML_3.98-1.1
[31] xtable_1.7-1
>

***** End Output and sessionInfo *****


Server Specifications/Features:
PowerEdge R910 Server
Processor 2x Intel Xeon E7-4860
Additional processor 2x Intel Xeon E7-4860
Memory 64GB
Red Hat Enterprise Linux Server 6.5


Thanks in advance,
Giovanni

Laboratory of Preclinical and Translational Research
IRCCS - CROB Oncology Referral Center of Basilicata
Rionero in Vulture - Basilicata - Italy

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