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 >>> 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/ >>> >> >> -- >> 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/ >> >> >> **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/
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