Thanks for pointing this out. I've updated the vignette to:
a <- fit$fitValleys$x[1];
b <- fit$fitValleys$x[2];
/H
On Mon, Mar 7, 2011 at 5:28 AM, Oscar Rueda <oscar.ru...@cancer.org.uk> wrote:
> Thanks a lot, Henrik!
>
> This has solved my problem.
> One more thing about the vignette: the code to call for confidence scores
> does not work for me:
>
>> a <- fit$x[1];
>> b <- fit$x[2];
>> cs[isDiploid] <- rowMins(abs(cbind(betaN[isDiploid]-a, betaN[isDiploid]-b)));
>
>> > Error in cs[isDiploid] <- rowMins(abs(cbind(betaN[isDiploid] - a,
> betaN[isDiploid] - :
> replacement has length zero
>
> The object fit I get looks like this:
>
>> fit
> [[1]]
> [[1]]$cn
> [1] 2
>
> [[1]]$nbrOfGenotypeGroups
> [1] 3
>
> [[1]]$fit
> type x density
> 1 peak 0.1228705 1.5184897
> 2 valley 0.3286780 0.5909177
> 3 peak 0.4792689 1.1727220
> 4 valley 0.6348794 0.5681927
> 5 peak 0.8356672 1.4166525
>
> [[1]]$fitValleys
> type x density
> 2 valley 0.3286780 0.5909177
> 4 valley 0.6348794 0.5681927
>
> [[1]]$n
> [1] 934063
>
>
> attr(,"class")
> [1] "NaiveGenotypeModelFit" "list"
>
> So there is no fit$x element. Anyway, I don't think I need these confidence
> scores for TumourBoost.
>
> Cheers,
> Oscar
>
>
> On 4/3/11 05:05, "Henrik Bengtsson" <henrik.bengts...@aroma-project.org>
> wrote:
>
>> Hi again,
>>
>> after receiving your data I could (i) reproduce the problem, and more
>> importantly (ii) fix the bug causing it. The reason was, as you
>> concluded, that in findPeaksAndValleys(x, to), when 'x' is a numeric,
>> argument 'to' was interpreted via partial argument matching as the
>> 'tol' argument instead of being passed on to density() via arguments
>> '...'. This was easily corrected by changing the order of 'tol' and
>> '...' from:
>>
>> findPeaksAndValleys.numeric <- function(x, tol=0, ..., na.rm=TRUE)
>>
>> to
>>
>> findPeaksAndValleys.numeric <- function(x, ..., tol=0, na.rm=TRUE)
>>
>> With your data, this simple fix will give the correct gender call with
>> and without argument 'to', i.e.
>>
>>> callXXorXY(betaN[is23], betaN[is24])
>> [1] "XX"
>>> callXXorXY(betaN[is23], betaN[is24], from=0, to=1)
>> [1] "XX"
>>
>>
>> I've committed the bug fix to aroma.light v1.18.4 (BioC release) as
>> well as aroma.light v1.19.4 (BioC devel). Until it's available there,
>> you can also install it from source by:
>>
>> source("http://aroma-project.org/hbLite.R";);
>> installPackages("http://www.braju.com/R/repos/aroma.light_1.18.4.tar.gz";) ;
>>
>>
>> Thanks.
>>
>> /Henrik
>>
>> On Mon, Feb 28, 2011 at 12:07 PM, Henrik Bengtsson
>> <henrik.bengts...@aroma-project.org> wrote:
>>> Y8l
>>>
>>> On Mon, Feb 28, 2011 at 4:09 AM, Oscar Rueda <oscar.ru...@cancer.org.uk>
>>> wrote:
>>>> HI,
>>>> Thanks for your answer.
>>>> I¹ve updated the packages, and I don¹t get the error in callXXorXY()
>>>> anymore.
>>>
>>> Good.
>>>
>>>> But I guess the problem with the arguments Ofrom¹ and Oto¹ is still
>>>> there:
>>>>
>>>>> callXXorXY(betaN[is23], betaN[is24], adjust=adjust, from=0, to=1);
>>>> [1] "XY"
>>>>> callXXorXY(betaN[is23], betaN[is24], adjust=adjust)
>>>> [1] "XX"
>>>>
>>>> When I try to run
>>>>
>>>>> isDiploid <- (!(is23 | is24));
>>>>>
>>>>> use <- which(isDiploid);
>>>>>
>>>>> muT <- callNaiveGenotypes(betaN[use], cn=2, adjust=adjust, from=0, to=1,
>>>>>
>>>>> verbose=less(verbose,10));
>>>>>
>>>>
>>>> I get
>>>>
>>>>>> + Error: nbrOfGenotypeGroups == 3 is not TRUE
>>>>>>
>>>>
>>>>
>>>> I know that this sample is female, so my guess is that Oto=1¹ gets a
>>>> partial
>>>> match with Otol¹ when passed to findPeaksAndValleys.density() and deletes
>>>> any peaks and valleys with density smaller than 1.
>>>
>>> Sorry, I missed your important point that arguments 'to' and 'tol' get
>>> mixed up; that's not good. Thanks for bringing it up again. I'll
>>> look into it. I'd also like to be able to reproduce exactly what
>>> you're getting. Would you mind fwd your data to me (you can do it
>>> offline)? The following should do:
>>>
>>> saveObject(list(betaN=betaN, is23=is23, is24=is24),
>>> "RuedaO_20110228,callXXorXY.RData");
>>>
>>> FYI, censoring/setting the range of the density estimate with 'to=0'
>>> and 'from=1' is slightly controversial because the BAFs can indeed be
>>> slightly outside [0,1] as well. This is because we allow for
>>> (slightly) negative (CA,CB) estimates. However, since the BAFs will
>>> only be slightly outside [0,1] I don't think this is a big issue (but
>>> it hasn't been fully investigated).
>>>
>>> Thxs
>>>
>>> /Henrik
>>>
>>>>
>>>> Thanks,
>>>> Oscar
>>>>
>>>> On 27/2/11 23:41, "Henrik Bengtsson" <henrik.bengts...@aroma-project.org>
>>>> wrote:
>>>>
>>>> Hi,
>>>>
>>>> thanks for reporting on this. Before doing anything else, try with
>>>> aroma.cn to v0.5.2;
>>>>
>>>> source("http://aroma-project.org/hbLite.R";);
>>>> hbInstall("aroma.cn");
>>>>
>>>>
>>>> From its NEWS file:
>>>>
>>>> Version: 0.5.2 [2010-08-04]
>>>> o Added option 'preserveScale' to TumorBoostNormalization for
>>>> correcting for signal compression in heterozygous SNPs.
>>>> The defaults is to do this correction.
>>>>
>>>> Version: 0.5.1 [2010-07-25]
>>>> o callXXorXY() no longer calls gender from chr Y when gender is
>>>> estimated as 'XX' from chr X.
>>>>
>>>> So, we actually made a change to the internal callXXorXY() that should
>>>> address the problems you are experiencing.
>>>>
>>>> Try to see if the above version solves your problem - if not, please
>>>> let us know again.
>>>>
>>>> /Henrik
>>>>
>>>> PS. aroma.cn v0.5.2 is actually a version from Aug 2010 that I forgot
>>>> to make publicly available; I've just uploaded to CRAN too.
>>>>
>>>>
>>>>
>>>>
>>>> On Wed, Feb 23, 2011 at 9:34 AM, Oscar Rueda <oscar.ru...@cancer.org.uk>
>>>> wrote:
>>>>> Dear all,
>>>>>
>>>>> I'm trying to run TumorBoost on a set of matched pairs. Like the vignette
>>>>> suggests, I have first run
>>>>>
>>>>> ds <- doASCRMAv2("TCGA,GBM", chipType="GenomeWideSNP_6,Full");
>>>>>
>>>>> Then I'm doing the naïve genotyping following all the steps in the
>>>>> vignette.
>>>>> But when I try to get the gender I get the following error
>>>>>
>>>>>> gender <- callXXorXY(betaN[is23], betaN[is24], adjust=adjust, from=0,
>>>>>> to=1);
>>>>> Error in list(`callXXorXY(betaN[is23], betaN[is24], adjust = adjust, from
>>>>> =
>>>>> 0,
>>>>> to = 1)` = <environment>, :
>>>>>
>>>>> [2011-02-23 16:22:05] Exception: Allele B fractions for ChrX and ChrY are
>>>>> inconsistent.
>>>>> at throw(Exception(...))
>>>>> at throw.default("Allele B fractions for ChrX and ChrY are
>>>>> inconsistent.")
>>>>> at throw("Allele B fractions for ChrX and ChrY are inconsistent.")
>>>>> at callXXorXY.numeric(betaN[is23], betaN[is24], adjust = adjust, from =
>>>>> 0,
>>>>> to
>>>>> at callXXorXY(betaN[is23], betaN[is24], adjust = adjust, from = 0, to =
>>>>> 1)
>>>>>
>>>>> I know that my samples are female, so I can set manually
>>>>>> gender <- "XX"
>>>>>
>>>>> But then I try to run the naïve genotyping and get another error:
>>>>>
>>>>>> muT <- callNaiveGenotypes(betaN[use], cn=2, adjust=adjust, from=0, to=1,
>>>>> verbose=less(verbose,10));
>>>>>
>>>>>>> + Error: nbrOfGenotypeGroups == 3 is not TRUE
>>>>>
>>>>>
>>>>> Taking a look at both errors I've seen that they come from the same
>>>>> function,
>>>>>
>>>>> fit <- findPeaksAndValleys(yT, adjust = adjust, ...)
>>>>>
>>>>> This function works OK if run directly on the BAFs of chromosome X (finds
>>>>> 3
>>>>> valleys and their peaks) but when we pass the argument 'from' and 'to',
>>>>> the
>>>>> argument 'to' is mistaken with argument 'tol', and as
>>>>> findPeaksAndValleys.density() does at the end
>>>>>
>>>>>> if (tol > 0) {
>>>>>> res <- subset(res, density >= tol)
>>>>>> }
>>>>>
>>>>>
>>>>> I don't get 3 peaks and 2 valleys anymore, but just 2 peaks (the ones with
>>>>> density values larger than 1). And the function returns the aforementioned
>>>>> error.
>>>>>
>>>>> So my question is; is it OK to run callXXorXY() and callNaiveGenotypes()
>>>>> removing the arguments 'from' and 'to'?
>>>>>
>>>>> My sessionInfo is:
>>>>>
>>>>>> sessionInfo()
>>>>> R version 2.12.0 (2010-10-15)
>>>>> Platform: x86_64-pc-linux-gnu (64-bit)
>>>>>
>>>>> locale:
>>>>> [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
>>>>> [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
>>>>> [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8
>>>>> [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
>>>>> [9] LC_ADDRESS=C LC_TELEPHONE=C
>>>>> [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
>>>>>
>>>>> attached base packages:
>>>>> [1] stats graphics grDevices utils datasets methods base
>>>>>
>>>>> other attached packages:
>>>>> [1] aroma.cn_0.5.0 aroma.core_2.0.0 aroma.light_1.18.3
>>>>> matrixStats_0.2.2
>>>>> [5] R.rsp_0.4.2 R.filesets_0.9.2 digest_0.4.2
>>>>> R.cache_0.4.0
>>>>> [9] R.utils_1.6.2 R.oo_1.7.5 R.methodsS3_1.2.1
>>>>>
>>>>> loaded via a namespace (and not attached):
>>>>> [1] affxparser_1.22.0
>>>>>>
>>>>>
>>>>> Thanks a lot,
>>>>> Oscar
>>>>>
>>>>>
>>>>> Oscar M. Rueda, PhD.
>>>>> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
>>>>> Cancer Research UK Cambridge Research Institute.
>>>>> Li Ka Shing Centre, Robinson Way.
>>>>> Cambridge CB2 0RE
>>>>> England
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> This communication is from Cancer Research UK. Our website is at
>>>>> www.cancerresearchuk.org. We are a registered charity in England and Wales
>>>>> (1089464) and in Scotland (SC041666) and a company limited by guarantee
>>>>> registered in England and Wales under number 4325234. Our registered
>>>>> address
>>>>> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central
>>>>> telephone number is 020 7242 0200.
>>>>>
>>>>> This communication and any attachments contain information which is
>>>>> confidential and may also be privileged. It is for the exclusive use of
>>>>> the intended recipient(s). If you are not the intended recipient(s)
>>>>> please
>>>>> note that any form of disclosure, distribution, copying or use of this
>>>>> communication or the information in it or in any attachments is strictly
>>>>> prohibited and may be unlawful. If you have received this communication
>>>>> in
>>>>> error, please notify the sender and delete the email and destroy any
>>>>> copies
>>>>> of it.
>>>>>
>>>>> E-mail communications cannot be guaranteed to be secure or error free, as
>>>>> information could be intercepted, corrupted, amended, lost, destroyed,
>>>>> arrive late or incomplete, or contain viruses. We do not accept liability
>>>>> for any such matters or their consequences. Anyone who communicates with
>>>>> us
>>>>> by e-mail is taken to accept the risks in doing so.
>>>>>
>>>>> --
>>>>> 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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>>>>>
>>>>
>>>>
>>>>
>>>> Oscar M. Rueda, PhD.
>>>> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
>>>> Cancer Research UK Cambridge Research Institute.
>>>> Li Ka Shing Centre, Robinson Way.
>>>> Cambridge CB2 0RE
>>>> England
>>>>
>>>>
>>>>
>>>> This communication is from Cancer Research UK. Our website is at
>>>> www.cancerresearchuk.org. We are a registered charity in England and Wales
>>>> (1089464) and in Scotland (SC041666) and a company limited by guarantee
>>>> registered in England and Wales under number 4325234. Our registered
>>>> address
>>>> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central
>>>> telephone number is 020 7242 0200.
>>>>
>>>> This communication and any attachments contain information which is
>>>> confidential and may also be privileged. It is for the exclusive use of the
>>>> intended recipient(s). If you are not the intended recipient(s) please note
>>>> that any form of disclosure, distribution, copying or use of this
>>>> communication or the information in it or in any attachments is strictly
>>>> prohibited and may be unlawful. If you have received this communication in
>>>> error, please notify the sender and delete the email and destroy any copies
>>>> of it.
>>>>
>>>> E-mail communications cannot be guaranteed to be secure or error free, as
>>>> information could be intercepted, corrupted, amended, lost, destroyed,
>>>> arrive late or incomplete, or contain viruses. We do not accept liability
>>>> for any such matters or their consequences. Anyone who communicates with us
>>>> by e-mail is taken to accept the risks in doing so.
>>>>
>>>> --
>>>> 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/
>>>>
>>>
>>
>
>
> Oscar M. Rueda, PhD.
> Postdoctoral Research Fellow, Breast Cancer Functional Genomics.
> Cancer Research UK Cambridge Research Institute.
> Li Ka Shing Centre, Robinson Way.
> Cambridge CB2 0RE
> England
>
>
>
>
> This communication is from Cancer Research UK. Our website is at
> www.cancerresearchuk.org. We are a registered charity in England and Wales
> (1089464) and in Scotland (SC041666) and a company limited by guarantee
> registered in England and Wales under number 4325234. Our registered address
> is Angel Building, 407 St John Street, London, EC1V 4AD. Our central
> telephone number is 020 7242 0200.
>
> This communication and any attachments contain information which is
> confidential and may also be privileged. It is for the exclusive use of the
> intended recipient(s). If you are not the intended recipient(s) please note
> that any form of disclosure, distribution, copying or use of this
> communication or the information in it or in any attachments is strictly
> prohibited and may be unlawful. If you have received this communication in
> error, please notify the sender and delete the email and destroy any copies
> of it.
>
> E-mail communications cannot be guaranteed to be secure or error free, as
> information could be intercepted, corrupted, amended, lost, destroyed, arrive
> late or incomplete, or contain viruses. We do not accept liability for any
> such matters or their consequences. Anyone who communicates with us by
> e-mail is taken to accept the risks in doing so.
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
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