Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor
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.utf8LC_TELEPHONE=en_US.utf8 [11] LC_MEASUREMENT=en_US.utf8LC_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_0.1.8affxparser_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_0.5.4R.cache_0.4.2 [10] R.filesets_1.0.2 digest_0.5.0 oligo_1.12.2 [13] oligoClasses_1.10.0Biobase_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_1.6.17preprocessCore_1.10.0 RSQLite_0.9-4 [10] splines_2.11.0survival_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
Re: Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor
Hi Jean-Paul, Thanks a lot for the info. Ying On Wed, Aug 31, 2011 at 5:46 AM, feugeas jean-paul jean-paul.feug...@sls.aphp.fr wrote: 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.utf8LC_TELEPHONE=en_US.utf8 [11] LC_MEASUREMENT=en_US.utf8LC_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_0.1.8affxparser_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_0.5.4R.cache_0.4.2 [10] R.filesets_1.0.2 digest_0.5.0 oligo_1.12.2 [13] oligoClasses_1.10.0Biobase_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_1.6.17preprocessCore_1.10.0 RSQLite_0.9-4 [10] splines_2.11.0survival_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
