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.
>>>>
>>>>
>>>> You received this message because you are subscribed to the Google Groups
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>>>> 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
>>> 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
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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To unsubscribe and other options, go to http://www.aroma-project.org/forum/
