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 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. 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/