Hi Rico,
using the RicoD_20111003.RData file [8021939 bytes] you've sent me:
> data <- loadObject("RicoD_20111003.RData");> str(data);'data.frame':
> 2458697 obs. of 5 variables: $ chromosome: int NA NA NA NA NA NA NA NA NA
> NA ... $ position : int NA NA NA NA NA NA NA NA NA NA ... $ betaN : num
> NaN NaN NaN NaN NaN NaN NaN NaN NaN NaN ... $ is23 : logi FALSE FALSE
> FALSE FALSE FALSE FALSE ... $ is24 : logi FALSE FALSE FALSE FALSE FALSE
> FALSE ...> attachLocally(data);
I conclude that the exception thrown by callXXorXY() is likely to be
correct, because there is something wrong with your allele B fractions
for the normal ('betaN'), because:
plotDensity(betaN[chromosome < 23])
does not show three clear modes as you would expect for normal
autosomal chromosomes (chr 1-19), cf. attached figure. Also, plotting
the normal BAFs along the genome indicates something is odd with your
data.
Could it be that you're looking at, say, a tumor sample?
/Henrik
On Tue, Oct 4, 2011 at 1:57 PM, Henrik Bengtsson
<henrik.bengts...@aroma-project.org> wrote:
> On Tue, Oct 4, 2011 at 6:46 AM, Rico.Daniel <dr...@cnio.es> wrote:
>> Dear Henrik,
>>
>> I am following this vignette:
>>
>> http://aroma-project.org/vignettes/naive-genotyping
>
> I see.
>
>>
>> I would be happy to send what you are asking for:
>>
>> data <- data.frame(chromosome=chromosome, position=position, betaN=betaN,
>> is23=is23, is24=is24);
>>
>> but chromosome and position objects are not created in this vignette... what
>> do you need?
>
> The just use:
>
> chromosome <- ugp[,1];
> position <- ugp[,1];
>
> /Henrik
>
>>
>> Thanks,
>> Daniel
>>
>> -----Original Message-----
>> From: aroma-affymetrix@googlegroups.com on behalf of Henrik Bengtsson
>> Sent: Mon 10/3/2011 9:04 PM
>> To: aroma-affymetrix@googlegroups.com
>> Subject: Re: [aroma.affymetrix] Naive Genotyping in Mouse
>>
>> Hi.
>>
>> On Mon, Oct 3, 2011 at 10:00 AM, Rico.Daniel <dr...@cnio.es> wrote:
>>> Hello, I am trying "Naive genotyping" with MOUSEDIVm520650 arrays. I am
>>> following the vignette
>>
>> Which one?
>>
>>> and 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>, :
>>>
>>> [2011-10-03 18:50:11] 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 callXX
>>
>> This may be a problem due to a particularly bad/noisy sample in
>> combination to our internal sanity checks. More below...
>>
>>>
>>> Following this thread:
>>> http://aroma-affymetrix.967894.n3.nabble.com/aroma-affymetrix-Problem-with-naive-genotyping-TumorBoost-vignette-td2561665.html
>>>
>>> I set gender manually:
>>> gender <- "XY"
>>>
>>> # Call genotypes
>>> naValue <- as.double(NA);
>>> fit <- NULL;
>>> mu <- rep(naValue, times=length(units));
>>> cs <- rep(naValue, times=length(units));
>>> # All but ChrX & ChrY in male
>>> isDiploid <- (!(is23 | is24));
>>> use <- which(isDiploid);
>>> muT <- callNaiveGenotypes( betaN[use], cn=2, adjust=adjust, from=0,
>>> to=1, verbose=less(verbose,10));
>>> # And get this error:
>>>
>>> Error: nbrOfGenotypeGroups == 3 is not TRUE
>>>
>>> I assume there should be three peaks in the betaN distribution, but I only
>>> see one peak at 0.2 in an unimodal distribution:
>>>
>>>> summary(betaN)
>>> Min. 1st Qu. Median Mean 3rd Qu. Max. NA's
>>> 0.0 0.1 0.2 0.3 0.3 1.0 1837467.0
>>>
>>> # (1837467 NA's would be the not polymorphic probes)
>>
>> So not sure what data you have in hand, but could you make the
>> following file available (e.g. http://min.us/) to me (off the mailing
>> list):
>>
>> data <- data.frame(chromosome=chromosome, position=position,
>> betaN=betaN, is23=is23, is24=is24);
>> saveObject(data, file="RicoD_20111003.RData");
>>
>> so that I can have a look at it. Maybe we need to add a fallback
>> strategy for callXXorXY() or at least add an option to manually add
>> the XX/XY status.
>>
>> /Henrik
>>
>>>
>>>
>>> I tried to follow the previous thread, but I could not find what is wrong
>>> with my data.
>>>
>>> Any help will be greatly appreciated!! (once more)
>>>
>>> Best,
>>> Daniel
>>>
>>>
>>>> sessionInfo()
>>> R version 2.13.0 (2011-04-13)
>>> Platform: x86_64-unknown-linux-gnu (64-bit)
>>>
>>> locale:
>>> [1] C
>>>
>>> attached base packages:
>>> [1] stats graphics grDevices utils datasets methods base
>>>
>>> other attached packages:
>>> [1] aroma.cn_0.8.2 aroma.core_2.2.0 aroma.light_1.20.0
>>> matrixStats_0.2.2
>>> [5] R.rsp_0.6.2 R.filesets_1.1.0 digest_0.5.0 R.cache_0.5.1
>>> [9] R.utils_1.7.8 R.oo_1.8.1 R.methodsS3_1.2.1
>>>
>>> loaded via a namespace (and not attached):
>>> [1] affxparser_1.24.0 tools_2.13.0
>>> Warning message:
>>> 'DESCRIPTION' file has 'Encoding' field and re-encoding is not possible
>>>
>>>
>>> ********************************************
>>>
>>> Daniel Rico Rodriguez, PhD.
>>> Structural Biology and BioComputing Programme
>>> Spanish National Cancer Research Center, CNIO
>>> Melchor Fernandez Almagro, 3.
>>> 28029 Madrid, Spain.
>>> Phone: +34 91 224 69 00 #3015
>>> dr...@cnio.es
>>> http://www.cnio.es
>>>
>>> ********************************************
>>>
>>>
>>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
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>>> --
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>>>
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>>
>> --
>> 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/
>>
>>
>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los
>> ficheros adjuntos, pueden contener información protegida para el uso
>> exclusivo de su destinatario. Se prohíbe la distribución, reproducción o
>> cualquier otro tipo de transmisión por parte de otra persona que no sea el
>> destinatario. Si usted recibe por error este correo, se ruega comunicarlo al
>> remitente y borrar el mensaje recibido.
>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may
>> contain confidential and privileged information for the sole use of the
>> designated recipient named above. Distribution, reproduction or any other
>> use of this transmission by any party other than the intended recipient is
>> prohibited. If you are not the intended recipient please contact the sender
>> and delete all copies.
>>
>>
>-- 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/
<<attachment: RicoD_20111003,betaN,chr1-19,density.png>>
