On Fri, Mar 7, 2014 at 8:05 AM, Damian Plichta wrote:
> Hi Henrik,
>
> Lowering memory helped - it's drinks on me when we meet.
>
> It has been running for approximately 7 days now ("ETA for unit type
> 'expression': 20140320 23:20:26"). With the updated affxparser can I speed
> it up by increasin
Hi Henrik,
Lowering memory helped - it's drinks on me when we meet.
It has been running for approximately 7 days now ("ETA for unit type
'expression': 20140320 23:20:26"). With the updated affxparser can I speed
it up by increasing the memory burden? The current memory allocation is
approxima
Did lowering "memory/ram" solve your problem?
Also, an updated version of affxparser that no longer should overflow
by the integer multiplication is available (on Bioconductor).
Cheers,
Henrik
On Thu, Feb 27, 2014 at 12:36 PM, Henrik Bengtsson
wrote:
> Congratulations Damian,
>
> I think your
Congratulations Damian,
I think your the first one to hit a limit of the Aroma Framework
(remind me to by you a drink whenever you see me in person).
I narrowed it down to the affxparser(*) package and I'll investigate
further on how to fix this. It should not occur and I'm confident
that it can
Hi Henrik,
Thank you, that was helpful.
I run to another problem though. I am trying to perform ExonRmaPlm(csQN,
merge=TRUE) but this produces a following error:
20140226 23:25:33| Identifying CDF cell indices...done
Error in vector("double", nbrOfCells * nbrOfArrays) :
vector size can
On Tue, Feb 18, 2014 at 7:30 PM, Damian Plichta
wrote:
> Thanks, that helped a lot. It took me less than 3 hours to perform the
> background correction.
>
> Now I'm wondering if for the next step, quantile normalization, I could do a
> similar trick. Is there a way to precompute the target empiric
Thanks, that helped a lot. It took me less than 3 hours to perform the
background correction.
Now I'm wondering if for the next step, quantile normalization, I could do
a similar trick. Is there a way to precompute the target empirical
distribution based on all arrays and then do the normalizat
Hi.
On Sun, Feb 16, 2014 at 6:53 PM, Damian Plichta
wrote:
> Hi,
>
> I'm processing around 5500 affymetrix exon arrays. The
> RmaBackgroundCorrection() is pretty slow, 1-2 minutes/array. I played with
> setOption(aromaSettings, "memory/ram", X) and increased X up to 100 but it
> didn't have any e
Hi,
I'm processing around 5500 affymetrix exon arrays.
The RmaBackgroundCorrection() is pretty slow, 1-2 minutes/array. I played
with setOption(aromaSettings, "memory/ram", X) and increased X up to 100
but it didn't have any effect on this stage of analysis.
Any way to speed the process up?
