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
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> > > To post to this group, send email to aroma-affymetrix@googlegroups.com
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> > >
> >
> > --
> > 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
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> > To post to this group, send email to aroma-affymetrix@googlegroups.com
> > To unsubscribe and other options, go to
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>
> --
> 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/.
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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
