Dear all, I'm trying to run TumorBoost on a set of matched pairs. Like the vignette suggests, I have first run
ds <- doASCRMAv2("TCGA,GBM", chipType="GenomeWideSNP_6,Full"); Then I'm doing the naïve genotyping following all the steps in the vignette. But when I try to get the gender I 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>, : [2011-02-23 16:22:05] 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 callXXorXY(betaN[is23], betaN[is24], adjust = adjust, from = 0, to = 1) I know that my samples are female, so I can set manually > gender <- "XX" But then I try to run the naïve genotyping and get another error: > muT <- callNaiveGenotypes(betaN[use], cn=2, adjust=adjust, from=0, to=1, verbose=less(verbose,10)); > > + Error: nbrOfGenotypeGroups == 3 is not TRUE Taking a look at both errors I've seen that they come from the same function, fit <- findPeaksAndValleys(yT, adjust = adjust, ...) This function works OK if run directly on the BAFs of chromosome X (finds 3 valleys and their peaks) but when we pass the argument 'from' and 'to', the argument 'to' is mistaken with argument 'tol', and as findPeaksAndValleys.density() does at the end > if (tol > 0) { > res <- subset(res, density >= tol) > } I don't get 3 peaks and 2 valleys anymore, but just 2 peaks (the ones with density values larger than 1). And the function returns the aforementioned error. So my question is; is it OK to run callXXorXY() and callNaiveGenotypes() removing the arguments 'from' and 'to'? My sessionInfo is: > sessionInfo() R version 2.12.0 (2010-10-15) Platform: x86_64-pc-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=C LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] aroma.cn_0.5.0 aroma.core_2.0.0 aroma.light_1.18.3 matrixStats_0.2.2 [5] R.rsp_0.4.2 R.filesets_0.9.2 digest_0.4.2 R.cache_0.4.0 [9] R.utils_1.6.2 R.oo_1.7.5 R.methodsS3_1.2.1 loaded via a namespace (and not attached): [1] affxparser_1.22.0 > Thanks a lot, Oscar Oscar M. Rueda, PhD. Postdoctoral Research Fellow, Breast Cancer Functional Genomics. Cancer Research UK Cambridge Research Institute. Li Ka Shing Centre, Robinson Way. Cambridge CB2 0RE England This communication is from Cancer Research UK. Our website is at www.cancerresearchuk.org. We are a registered charity in England and Wales (1089464) and in Scotland (SC041666) and a company limited by guarantee registered in England and Wales under number 4325234. Our registered address is Angel Building, 407 St John Street, London, EC1V 4AD. Our central telephone number is 020 7242 0200. This communication and any attachments contain information which is confidential and may also be privileged. It is for the exclusive use of the intended recipient(s). If you are not the intended recipient(s) please note that any form of disclosure, distribution, copying or use of this communication or the information in it or in any attachments is strictly prohibited and may be unlawful. If you have received this communication in error, please notify the sender and delete the email and destroy any copies of it. E-mail communications cannot be guaranteed to be secure or error free, as information could be intercepted, corrupted, amended, lost, destroyed, arrive late or incomplete, or contain viruses. We do not accept liability for any such matters or their consequences. Anyone who communicates with us by e-mail is taken to accept the risks in doing so. -- 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/