[aroma.affymetrix] Parameters Sent To DNAcopy Functions

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[aroma.affymetrix] Parameters Sent To DNAcopy Functions

Dario Strbenac
Hello,

I remember reading a while ago that you can pass in additional parameters to CbsModel, and they will get passed onto DNAcopy functions. However, it doesn't seem to be working for me. I don't want any segments less than 5 probes wide. However, the 8th segment is only 2 wide.

> model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2), min.width = 5)
> fit(model, force = TRUE)
There were 50 or more warnings (use warnings() to see the first 50)
> foldChangeTable <- getRegions(model)[[1]]
> foldChangeTable[1:10,]
   chromosome     start      stop    mean count                                                                                                            url
1           1     51599  14941584  0.1975  7929          http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A0-16430583
2           1  14944039  16878322 -0.3535  1163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A14750611-17071750
3           1  16878364  17215511 -0.0717   163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16844649-17249226
4           1  17217671  26830062 -0.3424  6070   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16256432-27791301
5           1  26830481  72541505  0.1856 28889   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A22259379-77112607
6           1  72541525  72583737  2.0660    45   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A72537304-72587958
7           1  72584492 101046159  0.1900 18772  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A69738325-103892326
8           1 101046857 101047369 -2.8866     2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A101046806-101047420
9           1 101047606 150822152  0.1841 15874  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A96070151-155799607
10          1 150822331 150852863  2.6550    31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A150819278-150855916

I don't think the warnings are related to my question, but here they are, anyway :

> warnings()
Warning messages:
1: In log(M, base = 2) : NaNs produced
2: In log(A, base = 2) : NaNs produced
3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
  array has repeated maploc positions

4: In log(M, base = 2) : NaNs produced
5: In log(A, base = 2) : NaNs produced
6: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
  array has repeated maploc positions
...                ...                ...

I'm using aroma.affymetrix 1.7.0 on R 2.12.0 alpha.

--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

--
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Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions

Henrik Bengtsson
Hi.

On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac
<[hidden email]> wrote:
> Hello,
>
> I remember reading a while ago that you can pass in additional parameters to CbsModel, and they will get passed onto DNAcopy functions. However, it doesn't seem to be working for me. I don't want any segments less than 5 probes wide. However, the 8th segment is only 2 wide.
>
>> model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2), min.width = 5)
>> fit(model, force = TRUE)

Your expectation that you should specify the extra parameters in the
setup of the CbsModel object follows the overall style of the aroma
framework.  However, in this particular case we haven't implemented
passing parameters that way.  However, a workaround is to do it via
the fit() call instead.  In your case, you would do:

model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2));
fit(model, min.width=5, force=TRUE);

Hope this helps

Henrik

> There were 50 or more warnings (use warnings() to see the first 50)
>> foldChangeTable <- getRegions(model)[[1]]
>> foldChangeTable[1:10,]
>   chromosome     start      stop    mean count                                                                                                            url
> 1           1     51599  14941584  0.1975  7929          http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A0-16430583
> 2           1  14944039  16878322 -0.3535  1163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A14750611-17071750
> 3           1  16878364  17215511 -0.0717   163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16844649-17249226
> 4           1  17217671  26830062 -0.3424  6070   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16256432-27791301
> 5           1  26830481  72541505  0.1856 28889   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A22259379-77112607
> 6           1  72541525  72583737  2.0660    45   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A72537304-72587958
> 7           1  72584492 101046159  0.1900 18772  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A69738325-103892326
> 8           1 101046857 101047369 -2.8866     2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A101046806-101047420
> 9           1 101047606 150822152  0.1841 15874  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A96070151-155799607
> 10          1 150822331 150852863  2.6550    31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A150819278-150855916
>
> I don't think the warnings are related to my question, but here they are, anyway :
>
>> warnings()
> Warning messages:
> 1: In log(M, base = 2) : NaNs produced
> 2: In log(A, base = 2) : NaNs produced
> 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
>  array has repeated maploc positions
>
> 4: In log(M, base = 2) : NaNs produced
> 5: In log(A, base = 2) : NaNs produced
> 6: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
>  array has repeated maploc positions
> ...                ...                ...
>
> I'm using aroma.affymetrix 1.7.0 on R 2.12.0 alpha.
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> --
> 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 [hidden email]
> 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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Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions

Dario Strbenac
Thanks for this.

---- Original message ----

>Date: Wed, 29 Sep 2010 20:14:03 -0700
>From: [hidden email] (on behalf of Henrik Bengtsson <[hidden email]>)
>Subject: Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions  
>To: aroma-affymetrix <[hidden email]>
>
>Hi.
>
>On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac
><[hidden email]> wrote:
>> Hello,
>>
>> I remember reading a while ago that you can pass in additional parameters to CbsModel, and they will get passed onto DNAcopy functions. However, it doesn't seem to be working for me. I don't want any segments less than 5 probes wide. However, the 8th segment is only 2 wide.
>>
>>> model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2), min.width = 5)
>>> fit(model, force = TRUE)
>
>Your expectation that you should specify the extra parameters in the
>setup of the CbsModel object follows the overall style of the aroma
>framework.  However, in this particular case we haven't implemented
>passing parameters that way.  However, a workaround is to do it via
>the fit() call instead.  In your case, you would do:
>
>model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2));
>fit(model, min.width=5, force=TRUE);
>
>Hope this helps
>
>Henrik
>
>> There were 50 or more warnings (use warnings() to see the first 50)
>>> foldChangeTable <- getRegions(model)[[1]]
>>> foldChangeTable[1:10,]
>>   chromosome     start      stop    mean count                                                                                                            url
>> 1           1     51599  14941584  0.1975  7929          http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A0-16430583
>> 2           1  14944039  16878322 -0.3535  1163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A14750611-17071750
>> 3           1  16878364  17215511 -0.0717   163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16844649-17249226
>> 4           1  17217671  26830062 -0.3424  6070   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16256432-27791301
>> 5           1  26830481  72541505  0.1856 28889   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A22259379-77112607
>> 6           1  72541525  72583737  2.0660    45   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A72537304-72587958
>> 7           1  72584492 101046159  0.1900 18772  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A69738325-103892326
>> 8           1 101046857 101047369 -2.8866     2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A101046806-101047420
>> 9           1 101047606 150822152  0.1841 15874  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A96070151-155799607
>> 10          1 150822331 150852863  2.6550    31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A150819278-150855916
>>
>> I don't think the warnings are related to my question, but here they are, anyway :
>>
>>> warnings()
>> Warning messages:
>> 1: In log(M, base = 2) : NaNs produced
>> 2: In log(A, base = 2) : NaNs produced
>> 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
>>  array has repeated maploc positions
>>
>> 4: In log(M, base = 2) : NaNs produced
>> 5: In log(A, base = 2) : NaNs produced
>> 6: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
>>  array has repeated maploc positions
>> ...                ...                ...
>>
>> I'm using aroma.affymetrix 1.7.0 on R 2.12.0 alpha.
>>
>> --------------------------------------
>> Dario Strbenac
>> Research Assistant
>> Cancer Epigenetics
>> Garvan Institute of Medical Research
>> Darlinghurst NSW 2010
>> Australia
>>
>> --
>> 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 [hidden email]
>> 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 [hidden email]
>To unsubscribe and other options, go to http://www.aroma-project.org/forum/


--------------------------------------
Dario Strbenac
Research Assistant
Cancer Epigenetics
Garvan Institute of Medical Research
Darlinghurst NSW 2010
Australia

--
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 [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/
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Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions

Henrik Bengtsson-4
Just a follow up on this thread and close it:

Starting with aroma.core v1.8.0 (2010-11-07) it is possible to specify
additional parameters when setting up the segmentation model,
parameters that will be passed to the actual segmentation method.  For
instance, (instead of having to pass them as arguments to fit(),  the
preferred way is now to do:

seg <- CbsModel(ds, min.width=5);
fit(seg);

This means that also:

seg <- CbsModel(ds, min.width=5);
ce <- ChromosomeExplorer(seg);
process(seg);

will also work (where fit() is called implicitly by process()).

Note that the aroma framework only pass on these optional arguments to
the underlying segmentation method.  In order to find out which they
are and what they do, see the specific segmentation method, e.g.
help("segment", package="DNAcopy").

/Henrik


On Wed, Sep 29, 2010 at 8:20 PM, Dario Strbenac
<[hidden email]> wrote:

> Thanks for this.
>
> ---- Original message ----
>>Date: Wed, 29 Sep 2010 20:14:03 -0700
>>From: [hidden email] (on behalf of Henrik Bengtsson <[hidden email]>)
>>Subject: Re: [aroma.affymetrix] Parameters Sent To DNAcopy Functions
>>To: aroma-affymetrix <[hidden email]>
>>
>>Hi.
>>
>>On Wed, Sep 29, 2010 at 8:00 PM, Dario Strbenac
>><[hidden email]> wrote:
>>> Hello,
>>>
>>> I remember reading a while ago that you can pass in additional parameters to CbsModel, and they will get passed onto DNAcopy functions. However, it doesn't seem to be working for me. I don't want any segments less than 5 probes wide. However, the 8th segment is only 2 wide.
>>>
>>>> model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2), min.width = 5)
>>>> fit(model, force = TRUE)
>>
>>Your expectation that you should specify the extra parameters in the
>>setup of the CbsModel object follows the overall style of the aroma
>>framework.  However, in this particular case we haven't implemented
>>passing parameters that way.  However, a workaround is to do it via
>>the fit() call instead.  In your case, you would do:
>>
>>model <- CbsModel(extract(normalisedCels, 1), extract(normalisedCels, 2));
>>fit(model, min.width=5, force=TRUE);
>>
>>Hope this helps
>>
>>Henrik
>>
>>> There were 50 or more warnings (use warnings() to see the first 50)
>>>> foldChangeTable <- getRegions(model)[[1]]
>>>> foldChangeTable[1:10,]
>>>   chromosome     start      stop    mean count                                                                                                            url
>>> 1           1     51599  14941584  0.1975  7929          http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A0-16430583
>>> 2           1  14944039  16878322 -0.3535  1163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A14750611-17071750
>>> 3           1  16878364  17215511 -0.0717   163   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16844649-17249226
>>> 4           1  17217671  26830062 -0.3424  6070   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A16256432-27791301
>>> 5           1  26830481  72541505  0.1856 28889   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A22259379-77112607
>>> 6           1  72541525  72583737  2.0660    45   http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A72537304-72587958
>>> 7           1  72584492 101046159  0.1900 18772  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A69738325-103892326
>>> 8           1 101046857 101047369 -2.8866     2 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A101046806-101047420
>>> 9           1 101047606 150822152  0.1841 15874  http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A96070151-155799607
>>> 10          1 150822331 150852863  2.6550    31 http://genome.ucsc.edu/cgi-bin/hgTracks?clade=vertebrate&org=Human&db=hg18&position=chr1%3A150819278-150855916
>>>
>>> I don't think the warnings are related to my question, but here they are, anyway :
>>>
>>>> warnings()
>>> Warning messages:
>>> 1: In log(M, base = 2) : NaNs produced
>>> 2: In log(A, base = 2) : NaNs produced
>>> 3: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
>>>  array has repeated maploc positions
>>>
>>> 4: In log(M, base = 2) : NaNs produced
>>> 5: In log(A, base = 2) : NaNs produced
>>> 6: In DNAcopy::CNA(genomdat = data$y, chrom = data$chromosome,  ... :
>>>  array has repeated maploc positions
>>> ...                ...                ...
>>>
>>> I'm using aroma.affymetrix 1.7.0 on R 2.12.0 alpha.
>>>
>>> --------------------------------------
>>> Dario Strbenac
>>> Research Assistant
>>> Cancer Epigenetics
>>> Garvan Institute of Medical Research
>>> Darlinghurst NSW 2010
>>> Australia
>>>
>>> --
>>> 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 [hidden email]
>>> 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 [hidden email]
>>To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
>
> --------------------------------------
> Dario Strbenac
> Research Assistant
> Cancer Epigenetics
> Garvan Institute of Medical Research
> Darlinghurst NSW 2010
> Australia
>
> --
> 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 [hidden email]
> 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 [hidden email]
To unsubscribe and other options, go to http://www.aroma-project.org/forum/