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
>
> ********************************************
>
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version of the package, 2) to report the output of sessionInfo() and
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