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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