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 > ficheros adjuntos, pueden contener información protegida para el uso > exclusivo de su destinatario. 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