Hi,
thanks for reporting on this. Before doing anything else, try with
aroma.cn to v0.5.2;
source("http://aroma-project.org/hbLite.R";);
hbInstall("aroma.cn");
>From its NEWS file:
Version: 0.5.2 [2010-08-04]
o Added option 'preserveScale' to TumorBoostNormalization for
correcting for signal compression in heterozygous SNPs.
The defaults is to do this correction.
Version: 0.5.1 [2010-07-25]
o callXXorXY() no longer calls gender from chr Y when gender is
estimated as 'XX' from chr X.
So, we actually made a change to the internal callXXorXY() that should
address the problems you are experiencing.
Try to see if the above version solves your problem - if not, please
let us know again.
/Henrik
PS. aroma.cn v0.5.2 is actually a version from Aug 2010 that I forgot
to make publicly available; I've just uploaded to CRAN too.
On Wed, Feb 23, 2011 at 9:34 AM, Oscar Rueda <oscar.ru...@cancer.org.uk> wrote:
> 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
>
>
>
>
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