Re: [aroma.affymetrix] Re: CbsModel parameters

[mbaudis]

Thanks for the parallel note! I knew it existed, but hadn't checked the 
implementation yet, deferring it to a soon-to-be-done pipeline review. 
However, the 

future::plan("multicore")

... makes it very simple; seems to work great.

Michael.

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Re: [aroma.affymetrix] Re: CbsModel parameters

[Henrik Bengtsson]

Hi,

I've bbc:ed Venkat since I don't know if he's on this list or not.

I don't have any particular suggestions for tweaking the default
DNAcopy::segment() CBS parameters.

If you missed it, both aroma.affymetrix and PSCBS now supports
parallel process to some extent, cf.
http://www.aroma-project.org/howtos/parallel_processing/

/Henrik


On Tue, Feb 2, 2016 at 6:28 AM, mbaudis  wrote:
> Hi Hendrik, Venkat,
>
> we're about to start a large processing run (>20k Affy arrays from GEO,
> various platforms). Good time to review/update our old pipeline ...
>
> What is the best way/recomm. parameters now for the min.width argument, and
> has the cbs part been modified? Any recommendation to do platform specific
> adjustements (majority are 250k & SNP6)?
>
> Pointers appreciated!
>
> Thanks & best,
>
> Michael.
>
> On Wednesday, October 27, 2010 at 9:19:24 PM UTC+2, Venkat wrote:
>>
>> This can happen occasionally.  The min.width argument specifies the
>> minimum number of probes in the minor arc of the circular (remember this is
>> circular binary segmentation).  So if you can get 2 probes from one end and
>> 3 from the other to be significantly different the middle you will get a
>> significant result and a segmentation.  I need to change the code in order
>> to eliminate this possibility.
>>
>> Venkat
>>
>>
>> On Wed, Oct 27, 2010 at 2:32 PM, Henrik Bengtsson
>>  wrote:
>>>
>>> Are you sure you are not picking up old results, that is, did you use
>>> fit(cbs, ..., force=TRUE) or simply did you remove the previous
>>> segmentation results in cbsData/?
>>>
>>> You can troubleshoot with one array and one chromosome, e.g.
>>>
>>> fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits="sdundo",
>>> undo.SD=1, force=TRUE, verbose=-10);
>>>
>>> /Henrik
>>>
>>> On Wed, Oct 27, 2010 at 11:20 AM, Kai  wrote:
>>> > Hi Henrik,
>>> >
>>> > Thank you for your reply. However, I followed your instructions but
>>> > still got segments with only 2 markers:
>>> >
>>> > These are the codes I ran:
>>> >
>>> > cbs = CbsModel(ds);
>>> > cbs$.calculateRatios = FALSE;
>>> > fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits="sdundo",
>>> > undo.SD=1, verbose=-10);
>>> > ce = ChromosomeExplorer(cbs);
>>> > process(ce,chromosomes=c(1:23));
>>> >
>>> > These are what I found out in the results (there are a total of 4
>>> > samples):
>>> >
>>> >> min(getRegions(cbs)[[1]][,5])
>>> > [1] 5
>>> >> min(getRegions(cbs)[[2]][,5])
>>> > [1] 2
>>> >> min(getRegions(cbs)[[3]][,5])
>>> > [1] 2
>>> >> min(getRegions(cbs)[[4]][,5])
>>> > [1] 2
>>> >> which(getRegions(cbs)[[4]][,5]==2)
>>> > [1]  52 139
>>> >> getRegions(cbs)[[4]][139,1:5]
>>> >chromosomestart stop   mean count
>>> > 139 16 45057510 45057696 -1.427 2
>>> >
>>> > It seems to me that min.width=5 worked only in the first sample. Do
>>> > you have any idea on this? Thanks!
>>> >
>>> > Best,
>>> > Kai
>>> >
>>> >
>>> > On Oct 26, 9:09 pm, Henrik Bengtsson >> > project.org> wrote:
>>> >> I forgot to say that in the next release of aroma.core package, you
>>> >> will be able to specify additional arguments when you setup the CBS
>>> >> model:
>>> >>
>>> >> cbs <- CbsModel(ds, min.width=5);
>>> >>
>>> >> ...but until then you have to stick with the below workaround.
>>> >>
>>> >> /Henrik
>>> >>
>>> >> On Tue, Oct 26, 2010 at 9:07 PM, hb  wrote:
>>> >> > Hi,
>>> >>
>>> >> > sorry my mistake. I meant to write that you should pass the
>>> >> > additional arguments to fit() for the CbsModel (not process()), e.g.
>>> >>
>>> >> > cbs <- CbsModel(ds);
>>> >> > cbs$.calculateRatios <- FALSE;
>>> >> > fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);
>>> >>
>>> >> > This will (explicitly) fit the segmentation model. Have a look at
>>> >> > the verbose output; you'll see that "min.width" should show up in the 
>>> >> > output
>>> >> > just before the DNAcopy segment() is called.
>>> >>
>>> >> > After you've done the segmentation for all of you arrays and
>>> >> > chromosomes, you can have the ChromosomeExplorer generate the report 
>>> >> > for you
>>> >> > as usual, i.e.
>>> >>
>>> >> > ce <- ChromosomeExplorer(cbs);
>>> >> > process(ce, chromosomes=1:23);
>>> >>
>>> >> > Note that in your case you have to either delete already generated
>>> >> > CBS results, or use fit(..., force=TRUE), in order for aroma.* not to 
>>> >> > pick
>>> >> > up the old segmentation. You also need to delete the already generated 
>>> >> > PNG
>>> >> > files for the ChromosomeExplorer under reports/...
>>> >>
>>> >> > On Tue, Oct 26, 2010 at 4:43 PM, Kai  wrote:
>>> >> >> Hi Henrik,
>>> >>
>>> >> >> Thank you very much for your response. However, I tried the
>>> >> >> following
>>> >> >> codes to set the minimal number of marker to 5, but the results I
>>> >> >> got
>>> >> >> still contain segments with only 2 markers ...
>>> >>
>>> >> >> cbs = 

Re: [aroma.affymetrix] Re: CbsModel parameters

[mbaudis]

Hi Hendrik, Venkat,

we're about to start a large processing run (>20k Affy arrays from GEO, 
various platforms). Good time to review/update our old pipeline ...

What is the best way/recomm. parameters now for the min.width argument, and 
has the cbs part been modified? Any recommendation to do platform specific 
adjustements (majority are 250k & SNP6)?

Pointers appreciated!

Thanks & best,

Michael.

On Wednesday, October 27, 2010 at 9:19:24 PM UTC+2, Venkat wrote:
>
> This can happen occasionally.  The min.width argument specifies the 
> minimum number of probes in the minor arc of the circular (remember this is 
> circular binary segmentation).  So if you can get 2 probes from one end and 
> 3 from the other to be significantly different the middle you will get a 
> significant result and a segmentation.  I need to change the code in order 
> to eliminate this possibility.
>
> Venkat
>
>
> On Wed, Oct 27, 2010 at 2:32 PM, Henrik Bengtsson <
> henrik.b...@aroma-project.org > wrote:
>
>> Are you sure you are not picking up old results, that is, did you use
>> fit(cbs, ..., force=TRUE) or simply did you remove the previous
>> segmentation results in cbsData/?
>>
>> You can troubleshoot with one array and one chromosome, e.g.
>>
>> fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits="sdundo",
>> undo.SD=1, force=TRUE, verbose=-10);
>>
>> /Henrik
>>
>> On Wed, Oct 27, 2010 at 11:20 AM, Kai  
>> wrote:
>> > Hi Henrik,
>> >
>> > Thank you for your reply. However, I followed your instructions but
>> > still got segments with only 2 markers:
>> >
>> > These are the codes I ran:
>> >
>> > cbs = CbsModel(ds);
>> > cbs$.calculateRatios = FALSE;
>> > fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits="sdundo",
>> > undo.SD=1, verbose=-10);
>> > ce = ChromosomeExplorer(cbs);
>> > process(ce,chromosomes=c(1:23));
>> >
>> > These are what I found out in the results (there are a total of 4
>> > samples):
>> >
>> >> min(getRegions(cbs)[[1]][,5])
>> > [1] 5
>> >> min(getRegions(cbs)[[2]][,5])
>> > [1] 2
>> >> min(getRegions(cbs)[[3]][,5])
>> > [1] 2
>> >> min(getRegions(cbs)[[4]][,5])
>> > [1] 2
>> >> which(getRegions(cbs)[[4]][,5]==2)
>> > [1]  52 139
>> >> getRegions(cbs)[[4]][139,1:5]
>> >chromosomestart stop   mean count
>> > 139 16 45057510 45057696 -1.427 2
>> >
>> > It seems to me that min.width=5 worked only in the first sample. Do
>> > you have any idea on this? Thanks!
>> >
>> > Best,
>> > Kai
>> >
>> >
>> > On Oct 26, 9:09 pm, Henrik Bengtsson > > project.org> wrote:
>> >> I forgot to say that in the next release of aroma.core package, you
>> >> will be able to specify additional arguments when you setup the CBS
>> >> model:
>> >>
>> >> cbs <- CbsModel(ds, min.width=5);
>> >>
>> >> ...but until then you have to stick with the below workaround.
>> >>
>> >> /Henrik
>> >>
>> >> On Tue, Oct 26, 2010 at 9:07 PM, hb  wrote:
>> >> > Hi,
>> >>
>> >> > sorry my mistake. I meant to write that you should pass the 
>> additional arguments to fit() for the CbsModel (not process()), e.g.
>> >>
>> >> > cbs <- CbsModel(ds);
>> >> > cbs$.calculateRatios <- FALSE;
>> >> > fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);
>> >>
>> >> > This will (explicitly) fit the segmentation model. Have a look at 
>> the verbose output; you'll see that "min.width" should show up in the 
>> output just before the DNAcopy segment() is called.
>> >>
>> >> > After you've done the segmentation for all of you arrays and 
>> chromosomes, you can have the ChromosomeExplorer generate the report for 
>> you as usual, i.e.
>> >>
>> >> > ce <- ChromosomeExplorer(cbs);
>> >> > process(ce, chromosomes=1:23);
>> >>
>> >> > Note that in your case you have to either delete already generated 
>> CBS results, or use fit(..., force=TRUE), in order for aroma.* not to pick 
>> up the old segmentation. You also need to delete the already generated PNG 
>> files for the ChromosomeExplorer under reports/...
>> >>
>> >> > On Tue, Oct 26, 2010 at 4:43 PM, Kai  wrote:
>> >> >> Hi Henrik,
>> >>
>> >> >> Thank you very much for your response. However, I tried the 
>> following
>> >> >> codes to set the minimal number of marker to 5, but the results I 
>> got
>> >> >> still contain segments with only 2 markers ...
>> >>
>> >> >> cbs = CbsModel(ds);
>> >> >> cbs$.calculateRatios = FALSE;
>> >> >> ce = ChromosomeExplorer(cbs);
>> >> >> process(ce,chromosomes=c(1:23),min.width=5);
>> >>
>> >> >> I am not clear where I should put "min.width=5"? If I do
>> >> >> "process(cbs,min.width=5)" first, how can I send the results to be
>> >> >> displayed by chromosome explorer?
>> >>
>> >> >> Thanks again for your help. I look forward to hearing from you soon.
>> >>
>> >> >> Best,
>> >> >> Kai
>> >>
>> >> >> On Sep 27, 9:47 pm, Henrik Bengtsson 
>> >> >> wrote:
>> >> >>> Hi.
>> >>
>> >> >>> On Mon, Sep 27, 2010 at 4:51 PM, Kai 

Re: [aroma.affymetrix] Re: CbsModel parameters

[Henrik Bengtsson]

Are you sure you are not picking up old results, that is, did you use
fit(cbs, ..., force=TRUE) or simply did you remove the previous
segmentation results in cbsData/?

You can troubleshoot with one array and one chromosome, e.g.

fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits=sdundo,
undo.SD=1, force=TRUE, verbose=-10);

/Henrik

On Wed, Oct 27, 2010 at 11:20 AM, Kai wangz...@gmail.com wrote:
 Hi Henrik,

 Thank you for your reply. However, I followed your instructions but
 still got segments with only 2 markers:

 These are the codes I ran:

 cbs = CbsModel(ds);
 cbs$.calculateRatios = FALSE;
 fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits=sdundo,
 undo.SD=1, verbose=-10);
 ce = ChromosomeExplorer(cbs);
 process(ce,chromosomes=c(1:23));

 These are what I found out in the results (there are a total of 4
 samples):

 min(getRegions(cbs)[[1]][,5])
 [1] 5
 min(getRegions(cbs)[[2]][,5])
 [1] 2
 min(getRegions(cbs)[[3]][,5])
 [1] 2
 min(getRegions(cbs)[[4]][,5])
 [1] 2
 which(getRegions(cbs)[[4]][,5]==2)
 [1]  52 139
 getRegions(cbs)[[4]][139,1:5]
    chromosome    start     stop   mean count
 139         16 45057510 45057696 -1.427     2

 It seems to me that min.width=5 worked only in the first sample. Do
 you have any idea on this? Thanks!

 Best,
 Kai


 On Oct 26, 9:09 pm, Henrik Bengtsson henrik.bengts...@aroma-
 project.org wrote:
 I forgot to say that in the next release of aroma.core package, you
 will be able to specify additional arguments when you setup the CBS
 model:

 cbs - CbsModel(ds, min.width=5);

 ...but until then you have to stick with the below workaround.

 /Henrik

 On Tue, Oct 26, 2010 at 9:07 PM, hb h...@biostat.ucsf.edu wrote:
  Hi,

  sorry my mistake. I meant to write that you should pass the additional 
  arguments to fit() for the CbsModel (not process()), e.g.

  cbs - CbsModel(ds);
  cbs$.calculateRatios - FALSE;
  fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);

  This will (explicitly) fit the segmentation model. Have a look at the 
  verbose output; you'll see that min.width should show up in the output 
  just before the DNAcopy segment() is called.

  After you've done the segmentation for all of you arrays and chromosomes, 
  you can have the ChromosomeExplorer generate the report for you as usual, 
  i.e.

  ce - ChromosomeExplorer(cbs);
  process(ce, chromosomes=1:23);

  Note that in your case you have to either delete already generated CBS 
  results, or use fit(..., force=TRUE), in order for aroma.* not to pick up 
  the old segmentation. You also need to delete the already generated PNG 
  files for the ChromosomeExplorer under reports/...

  On Tue, Oct 26, 2010 at 4:43 PM, Kai wangz...@gmail.com wrote:
  Hi Henrik,

  Thank you very much for your response. However, I tried the following
  codes to set the minimal number of marker to 5, but the results I got
  still contain segments with only 2 markers ...

  cbs = CbsModel(ds);
  cbs$.calculateRatios = FALSE;
  ce = ChromosomeExplorer(cbs);
  process(ce,chromosomes=c(1:23),min.width=5);

  I am not clear where I should put min.width=5? If I do
  process(cbs,min.width=5) first, how can I send the results to be
  displayed by chromosome explorer?

  Thanks again for your help. I look forward to hearing from you soon.

  Best,
  Kai

  On Sep 27, 9:47 pm, Henrik Bengtsson henrik.bengts...@gmail.com
  wrote:
  Hi.

  On Mon, Sep 27, 2010 at 4:51 PM, Kai wangz...@gmail.com wrote:
   Hi Henrik,

   I was wondering whether there is a way I can fine tune the behavior of
   CbsModel. Sometimes the default algorithm produces too many small
   fragments right next to each other without much separation in mean
   copy numbers. Is there a way to control how smooth the segmentation
   results are?

  Any additional arguments (in ...) that you pass to process(cbs, ...)
  will be passed down to the DNAcopy::segment(), which is the function
  doing the actual segmentation.  For more details on how fine tuning
  the CBS algorithm, see help(segment, package=DNAcopy).  You may
  also want to contact the authors of that method/package.

  /Henrik

   Thanks a lot!

   Best,
   Kai

   --
   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 websitehttp://www.aroma-project.org/.
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   tohttp://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 
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Re: [aroma.affymetrix] Re: CbsModel parameters

[Venkatraman Seshan]

This can happen occasionally.  The min.width argument specifies the minimum
number of probes in the minor arc of the circular (remember this is circular
binary segmentation).  So if you can get 2 probes from one end and 3 from
the other to be significantly different the middle you will get a
significant result and a segmentation.  I need to change the code in order
to eliminate this possibility.

Venkat


On Wed, Oct 27, 2010 at 2:32 PM, Henrik Bengtsson 
henrik.bengts...@aroma-project.org wrote:

 Are you sure you are not picking up old results, that is, did you use
 fit(cbs, ..., force=TRUE) or simply did you remove the previous
 segmentation results in cbsData/?

 You can troubleshoot with one array and one chromosome, e.g.

 fit(cbs, arrays=6, chromosomes=16, min.width=5, undo.splits=sdundo,
 undo.SD=1, force=TRUE, verbose=-10);

 /Henrik

 On Wed, Oct 27, 2010 at 11:20 AM, Kai wangz...@gmail.com wrote:
  Hi Henrik,
 
  Thank you for your reply. However, I followed your instructions but
  still got segments with only 2 markers:
 
  These are the codes I ran:
 
  cbs = CbsModel(ds);
  cbs$.calculateRatios = FALSE;
  fit(cbs, chromosomes=c(1:23), min.width=5, undo.splits=sdundo,
  undo.SD=1, verbose=-10);
  ce = ChromosomeExplorer(cbs);
  process(ce,chromosomes=c(1:23));
 
  These are what I found out in the results (there are a total of 4
  samples):
 
  min(getRegions(cbs)[[1]][,5])
  [1] 5
  min(getRegions(cbs)[[2]][,5])
  [1] 2
  min(getRegions(cbs)[[3]][,5])
  [1] 2
  min(getRegions(cbs)[[4]][,5])
  [1] 2
  which(getRegions(cbs)[[4]][,5]==2)
  [1]  52 139
  getRegions(cbs)[[4]][139,1:5]
 chromosomestart stop   mean count
  139 16 45057510 45057696 -1.427 2
 
  It seems to me that min.width=5 worked only in the first sample. Do
  you have any idea on this? Thanks!
 
  Best,
  Kai
 
 
  On Oct 26, 9:09 pm, Henrik Bengtsson henrik.bengts...@aroma-
  project.org wrote:
  I forgot to say that in the next release of aroma.core package, you
  will be able to specify additional arguments when you setup the CBS
  model:
 
  cbs - CbsModel(ds, min.width=5);
 
  ...but until then you have to stick with the below workaround.
 
  /Henrik
 
  On Tue, Oct 26, 2010 at 9:07 PM, hb h...@biostat.ucsf.edu wrote:
   Hi,
 
   sorry my mistake. I meant to write that you should pass the additional
 arguments to fit() for the CbsModel (not process()), e.g.
 
   cbs - CbsModel(ds);
   cbs$.calculateRatios - FALSE;
   fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);
 
   This will (explicitly) fit the segmentation model. Have a look at the
 verbose output; you'll see that min.width should show up in the output
 just before the DNAcopy segment() is called.
 
   After you've done the segmentation for all of you arrays and
 chromosomes, you can have the ChromosomeExplorer generate the report for you
 as usual, i.e.
 
   ce - ChromosomeExplorer(cbs);
   process(ce, chromosomes=1:23);
 
   Note that in your case you have to either delete already generated CBS
 results, or use fit(..., force=TRUE), in order for aroma.* not to pick up
 the old segmentation. You also need to delete the already generated PNG
 files for the ChromosomeExplorer under reports/...
 
   On Tue, Oct 26, 2010 at 4:43 PM, Kai wangz...@gmail.com wrote:
   Hi Henrik,
 
   Thank you very much for your response. However, I tried the following
   codes to set the minimal number of marker to 5, but the results I got
   still contain segments with only 2 markers ...
 
   cbs = CbsModel(ds);
   cbs$.calculateRatios = FALSE;
   ce = ChromosomeExplorer(cbs);
   process(ce,chromosomes=c(1:23),min.width=5);
 
   I am not clear where I should put min.width=5? If I do
   process(cbs,min.width=5) first, how can I send the results to be
   displayed by chromosome explorer?
 
   Thanks again for your help. I look forward to hearing from you soon.
 
   Best,
   Kai
 
   On Sep 27, 9:47 pm, Henrik Bengtsson henrik.bengts...@gmail.com
   wrote:
   Hi.
 
   On Mon, Sep 27, 2010 at 4:51 PM, Kai wangz...@gmail.com wrote:
Hi Henrik,
 
I was wondering whether there is a way I can fine tune the
 behavior of
CbsModel. Sometimes the default algorithm produces too many small
fragments right next to each other without much separation in mean
copy numbers. Is there a way to control how smooth the
 segmentation
results are?
 
   Any additional arguments (in ...) that you pass to process(cbs,
 ...)
   will be passed down to the DNAcopy::segment(), which is the function
   doing the actual segmentation.  For more details on how fine tuning
   the CBS algorithm, see help(segment, package=DNAcopy).  You may
   also want to contact the authors of that method/package.
 
   /Henrik
 
Thanks a lot!
 
Best,
Kai
 
--
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.
 

Re: [aroma.affymetrix] Re: CbsModel parameters

[Henrik Bengtsson]

Hi,

sorry my mistake.  I meant to write that you should pass the
additional arguments to fit() for the CbsModel (not process()), e.g.

cbs - CbsModel(ds);
cbs$.calculateRatios - FALSE;
fit(cbs, chromosomes=1:23, min.width=5, verbose=-10);

This will (explicitly) fit the segmentation model.  Have a look at the
verbose output; you'll see that min.width should show up in the
output just before the DNAcopy segment() is called.

After you've done the segmentation for all of you arrays and
chromosomes, you can have the ChromosomeExplorer generate the report
for you as usual, i.e.

ce - ChromosomeExplorer(cbs);
process(ce, chromosomes=1:23);

Note that in your case you have to either delete already generated CBS
results, or use fit(..., force=TRUE), in order for aroma.* not to pick
up the old segmentation.   You also need to delete the already
generated PNG files for the ChromosomeExplorer under reports/...




On Tue, Oct 26, 2010 at 4:43 PM, Kai wangz...@gmail.com wrote:
 Hi Henrik,

 Thank you very much for your response. However, I tried the following
 codes to set the minimal number of marker to 5, but the results I got
 still contain segments with only 2 markers ...

 cbs = CbsModel(ds);
 cbs$.calculateRatios = FALSE;
 ce = ChromosomeExplorer(cbs);
 process(ce,chromosomes=c(1:23),min.width=5);

 I am not clear where I should put min.width=5? If I do
 process(cbs,min.width=5) first, how can I send the results to be
 displayed by chromosome explorer?

 Thanks again for your help. I look forward to hearing from you soon.

 Best,
 Kai



 On Sep 27, 9:47 pm, Henrik Bengtsson henrik.bengts...@gmail.com
 wrote:
 Hi.

 On Mon, Sep 27, 2010 at 4:51 PM, Kai wangz...@gmail.com wrote:
  Hi Henrik,

  I was wondering whether there is a way I can fine tune the behavior of
  CbsModel. Sometimes the default algorithm produces too many small
  fragments right next to each other without much separation in mean
  copy numbers. Is there a way to control how smooth the segmentation
  results are?

 Any additional arguments (in ...) that you pass to process(cbs, ...)
 will be passed down to the DNAcopy::segment(), which is the function
 doing the actual segmentation.  For more details on how fine tuning
 the CBS algorithm, see help(segment, package=DNAcopy).  You may
 also want to contact the authors of that method/package.

 /Henrik



  Thanks a lot!

  Best,
  Kai

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


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