Hi Ying,
My PC works with Ubuntu Lucid, RAM 7.8 GB, 2 processors 2.93GHz, available disk
space 179 GiB (total disk space : 1 Tera)
Sincerly
Jean-Paul
----- Message d'origine -----
De: sean nj <njs...@gmail.com>
Date: Mardi, Août 30, 2011 4:30 pm
Objet: Re: Re : Re: [aroma.affymetrix] RAM scale factor
À: aroma-affymetrix@googlegroups.com
> Hi Jean-Paul,
>
> I have an off-topic question for you. I see you do analysis of more than
> 3000 arrays at once and you run linux on PC. Would you please tell me
> what
> the specification of your computer (CPU, RAM,..)? I also plan to do analysis
> of thousands of arrays at once and try to figure out if my computer can
> handle it or not.
>
> Thanks,
>
> Ying
>
> On Mon, Aug 29, 2011 at 9:01 AM, feugeas jean-paul <
> jean-paul.feug...@sls.aphp.fr> wrote:
>
> > Hello,
> > thank you very much for your answer. I have now found a way to
> increase the
> > RAM scale factor.
> > It actually works when I write the RAM scale factor inside the function
> > like this :
> > fit(plm,ram=50,verbose=verbose)
> > But it does not work If I write the RAM scale factor like this :
> > setOption(aromaSettings,"memory/ram",50.0)
> > fit(plm,verbose=verbose)
> > In that case it always takes 1 as RAM scale factor.
> > Sincerly yours
> > Jean-Paul
> >
> >
> > For information, here is my sessioninfo()
> > R version 2.11.0 (2010-04-22)
> > x86_64-pc-linux-gnu
> >
> > locale:
> > [1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
> > [3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
> > [5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
> > [7] LC_PAPER=en_US.utf8 LC_NAME=en_US.utf8
> > [9] LC_ADDRESS=en_US.utf8 LC_TELEPHONE=en_US.utf8
> > [11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=en_US.utf8
> >
> > attached base packages:
> > [1] stats graphics grDevices utils datasets methods base
> >
> > other attached packages:
> > [1] aroma.affymetrix_2.1.0 aroma.apd_0.1.8 affxparser_1.20.0
> > [4] R.huge_0.2.2 aroma.core_2.1.0 aroma.light_1.20.0
> > [7] matrixStats_0.2.2 R.rsp_0.5.4 R.cache_0.4.2
> > [10] R.filesets_1.0.2 digest_0.5.0 oligo_1.12.2
> > [13] oligoClasses_1.10.0 Biobase_2.8.0 R.utils_1.7.5
> > [16] R.oo_1.8.0 R.methodsS3_1.2.1 rkward_0.5.3
> >
> > loaded via a namespace (and not attached):
> > [1] affyio_1.16.0 annotate_1.26.1 AnnotationDbi_1.10.2
> > [4] Biostrings_2.16.9 DBI_0.2-5 genefilter_1.30.0
> > [7] IRanges_1.6.17 preprocessCore_1.10.0 RSQLite_0.9-4
> > [10] splines_2.11.0 survival_2.35-8 tools_2.11.0
> > [13] xtable_1.5-6
> >
> > >
> >
> >
> > ----- Message d'origine -----
> > De: Henrik Bengtsson <henrik.bengts...@aroma-project.org>
> > Date: Dimanche, Août 28, 2011 2:02 am
> > Objet: Re: [aroma.affymetrix] RAM scale factor
> > À: aroma-affymetrix@googlegroups.com
> >
> >
> > > Hi,
> > >
> > > sorry for the delay. This should work, but before diving into serious
> > > troubleshooting, could you please report your sessionInfo() so we
> know
> > > which versions of packages etc you are using?
> > >
> > > /Henrik
> > >
> > > On Wed, Aug 17, 2011 at 4:38 AM, feugeas jean-paul
> > > <jean-paul.feug...@sls.aphp.fr> wrote:
> > > > Hello,
> > > > I am currently trying to analyze data from 3223 arrays (expression
> > > arrays, U133 plus 2) with the following code :
> > > >
> > > > verbose<-Arguments$getVerbose(-8,timestamp=TRUE)
> > > > setOption(aromaSettings,"memory/ram",300.0)
> > > >
> > cdf<-AffymetrixCdfFile$fromFile("/media/lapino/Rabitt/compilation/ThBigCompil/2_arrays/annotationData/chipTypes/HG-U133_Plus_2/HG-U133_Plus_2.cdf")
> > > > cs <- AffymetrixCelSet$byName("jp", cdf=cdf)
> > > > bc <- GcRmaBackgroundCorrection(cs,type="affinities");
> > > > csB <- process(bc,verbose=verbose);
> > > > qn <- QuantileNormalization(csB, typesToUpdate="pm");
> > > > csN <- process(qn);
> > > > plm <- RmaPlm(csN, flavor="oligo");
> > > > fit(plm,verbose=verbose)
> > > >
> > > > at that point, the number of chunks is always 866 as it was with
> a
> > > RAM scale factor = 1 although RAM scale factor = 300 as it is
> > > indicated here :
> > > >
> > > > RmaPlm:
> > > > Data set: jp
> > > > Chip type: HG-U133_Plus_2
> > > > Input tags: GRBC,QN
> > > > Output tags: GRBC,QN,RMA,oligo
> > > > Parameters: (probeModel: chr "pm"; shift: num 0; flavor: chr
> > > "oligo"; treatNAsAs: chr "weights").
> > > > Path: plmData/jp,GRBC,QN,RMA,oligo/HG-U133_Plus_2
> > > > RAM: 0.01MB
> > > > 20110817 13:01:43| Started: 20110817 12:17:56
> > > > 20110817 13:01:43| Estimated time left: 37862.0min
> > > > 20110817 13:01:43| ETA: 20110912 20:03:41
> > > > 20110817 13:01:43| Fitting chunk #1 of 866...done
> > > > 20110817 13:01:43| Fitting chunk #2 of 866...
> > > > 20110817 13:01:43| Units:
> > > > int [1:62] 1055 1056 1057 1058 1059 1060 1061 1062 1063 1064 ...
> > > > 20110817 13:01:43| Reading probe intensities from 3223 arrays...
> > > > 20110817 13:01:43| Identifying CDF cell indices...
> > > >
> > > >
> > > > Is there a mean to reduce the number of chunks ?
> > > >
> > > > Thank you in advance for your help
> > > >
> > > > Sincerly yours
> > > >
> > > > Jean-Paul
> > > >
> > > > --
> > > > When reporting problems on aroma.affymetrix, make sure 1) to run
> the
> > > latest version of the package, 2) to report the output of
> > > sessionInfo() and traceback(), and 3) to post a complete code example.
> > > >
> > > >
> > > > You received this message because you are subscribed to the Google
> > > Groups "aroma.affymetrix" group with website
> > http://www.aroma-project.org/.
> > > > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > > > To unsubscribe and other options, go to
> > http://www.aroma-project.org/forum/
> > > >
> > >
> > > --
> > > When reporting problems on aroma.affymetrix, make sure 1) to run the
> > > latest version of the package, 2) to report the output of
> > > sessionInfo() and traceback(), and 3) to post a complete code example.
> > >
> > >
> > > You received this message because you are subscribed to the Google
> > > Groups "aroma.affymetrix" group with website
> > http://www.aroma-project.org/.
> > > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > > To unsubscribe and other options, go to
> > http://www.aroma-project.org/forum/
> >
> > --
> > When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest
> > version of the package, 2) to report the output of sessionInfo() and
> > traceback(), and 3) to post a complete code example.
> >
> >
> > You received this message because you are subscribed to the Google Groups
> > "aroma.affymetrix" group with website http://www.aroma-project.org/.
> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go to
> > http://www.aroma-project.org/forum/
> >
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the
> latest version of the package, 2) to report the output of
> sessionInfo() and traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google
> Groups "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
