Hi Gavin,

I'm afraid that particular error means nothing to me.  Does R exit too, or
does BASH stop and return you to an interactive session?

I found this very old post on R exit codes (
http://tolstoy.newcastle.edu.au/R/help/02b/3168.html), which may be relevant
but I'm speculating at the moment.

Is there anything particularly unusual with the 53rd array?  If you try to
BASH that array in isolation e.g. BASHoutput <- BASH(beadData, array=53)
does it proceed ok?

If it is a memory problem then it may be worth waiting for the next
Bioconductor release in about a week.  I recently discovered a memory leak
and a small bug that could cause a segfault in the BASH C code, which I've
patched in the developmental version.  I conducted a test this morning with
4 HumanV3 sections and the memory leak was about 100MB, which isn't ideal,
but with a 16GB limit I'd have thought you'd have enough head room not to be
affected by it.

Personally I've never tried to BASH so many sections in one go, but there's
reason it shouldn't work (memory and time permitting).  What we tend to do
is read a smaller number of sections (say a single BeadChip) into an R
session and process each in separately.  We then save each separate object
once it's been processed, load them all into a new R session and use the
combine() function to create a single beadLevelData object.  That way it can
be done in sort of coarse grained parallel.

As far as making it parallel in a more friendly way, that's something we're
working on, but it's not an imminent release.

I hope that's some help,


On Mon, Apr 4, 2011 at 9:51 PM, Gavin Koh <gavin.koh@gmail.com> wrote:

> I have 60 samples which were run on an Illumina HumanWG-6 v3.0
> Expression BeadChip (so 120 sections) and I am doing the
> pre-processing using beadarray.
>
> I am trying to generate spatial masks using BASH(). I have
> successfully run a smaller analysis (one slide of 12 sections) on my
> MacBook OSX Snow Leopard with 4Gb RAM using beadarray 2.7.
>
> The command I used to call BASH was:
> BASHoutput <- BASH(beadData, array=1:n)
>
> I am running the full analysis (120 sections) on a computing cluster
> (lustre). I have only requested a single core with 16Gb RAM, because I
> don't know how to get BASH() to multithread (although in theory it
> ought to be possible? it is a repetitive process after all). I cannot
> get the script past 53 sections, without bash() terminating with exit
> code "user code 2". Doesn't matter if I am running it interactively or
> calling R CMD BATCH. I don't know what the exit code means, so I don't
> know how to fix it. I don't think it is out of memory, because lustre
> has other codes for reporting out-of-memory and R usually reports
> out-of-memory errors as "cannot allocate vector of size..."? Also, the
> previous time it ran out of memory (when I tried 6 Gb RAM), it was
> lustre that terminated the process.
>
> I don't know if the problem is that BASH() cannot handle so many
> sections. If that is in fact the problem, then there are two solutions
> I can think of: 1. get BASH() to run multithreaded, or 2. run BASH()
> on selected sections only.
>
> On inspection of the pseudoimages, I can see there are only two
> sections of the 120 with obvious spatial defects (they look like
> scratches). Is it possible to find outliers on the other sections
> using the usual (faster) method (>3MAD) and then just use BASH() for
> the two sections that are defective only? or...is there a tool to just
> draw the masks myself??
>
> Thanks in advance,
>
> Gavin
>
> sessionInfo() reports:
> R version 2.12.0 (2010-10-15)
> Platform: x86_64-unknown-linux-gnu (64-bit)
>
> locale:
>  [1] LC_CTYPE=en_GB.UTF-8       LC_NUMERIC=C
>  [3] LC_TIME=en_GB.UTF-8        LC_COLLATE=en_GB.UTF-8
>  [5] LC_MONETARY=C              LC_MESSAGES=C
>  [7] LC_PAPER=en_GB.UTF-8       LC_NAME=C
>  [9] LC_ADDRESS=C               LC_TELEPHONE=C
> [11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
>
> attached base packages:
> [1] stats     graphics  grDevices utils     datasets  methods   base
>
> other attached packages:
> [1] beadarray_2.0.6 Biobase_2.10.0
>
> loaded via a namespace (and not attached):
> [1] limma_3.6.6
>
> --
> Hofstadter's Law: It always takes longer than you expect, even when
> you take into account Hofstadter's Law.
> —Douglas Hofstadter (in Gödel, Escher, Bach, 1979)
>
> _______________________________________________
> Bioconductor mailing list
> Bioconductor@r-project.org
> https://stat.ethz.ch/mailman/listinfo/bioconductor
> Search the archives:
> http://news.gmane.org/gmane.science.biology.informatics.conductor




-- 
Mike Smith
PhD Student
Computational Biology Group
Cambridge University

	[[alternative HTML version deleted]]

