Re : Re: Re : Re: [aroma.affymetrix] RAM scale factor

2011-08-31 Thread feugeas jean-paul
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

2011-08-31 Thread sean nj
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

Re: Re : Re: [aroma.affymetrix] RAM scale factor

2011-08-30 Thread sean nj
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 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, 

Re: Re : Re: [aroma.affymetrix] RAM scale factor

2011-08-29 Thread Henrik Bengtsson
Hi,

if you do:

library(aroma.affymetrix);
setOption(aromaSettings,memory/ram, 50.0);
ram - getOption(aromaSettings,memory/ram);
print(ram);

do you get NULL or 50.0?  My guess is NULL, which would explain it.
If so, try to update the aroma framework (minor fixed have been done
recently) by:

source(http://www.braju.com/R/hbLite.R;);
hbInstall(aroma.affymetrix);

BTW, you're running a rather old version of R - I recommend that you
update it.  Lots of (good) things
[http://cran.r-project.org/src/base/NEWS] have changed since.

/Henrik


On Mon, Aug 29, 2011 at 6:01 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