Hello, I am trying "Naive genotyping" with MOUSEDIVm520650 arrays. I am
following the vignette 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
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)
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
[email protected]
http://www.cnio.es
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