Dear Henrik,
I have been doing paired PSCBS analysis on a Genome Wide SNP array 6.0
data set in order to estimate LOH for 20 pairs of samples.
The code on the aroma web site successfully estimated LOH for most
pairs, while it fails to estimate LOH for several bad pairs.
An error message I got from a bad pair is :
>fit <- callLOH(fit, verbose=verbose);
Error: muC1atNonAB < muC1atAB is not TRUE
The code, which is not exactly the same as my actual one, that I use
is as follows:
===============================================
library("aroma.affymetrix");
verbose <- Arguments$getVerbose(-10, timestamp=TRUE);
library("PSCBS");
res <- doASCRMAv2(csR, verbose=verbose);
data <- extractPSCNArray(res$total);
# Total CNs for the tumor relative to the matched normal
CT <- 2 * (data[,"total","T"] / data[,"total","N"]);
# Allele B fractions for the tumor
betaT <- data[,"fracB","T"];
# Allele B fractions for the normal
betaN <- data[,"fracB","N"];
# Get (chromosome, position) annotation data
ugp <- getAromaUgpFile(res$total);
chromosome <- ugp[,1,drop=TRUE];
x <- ugp[,2,drop=TRUE];
# Setup data structure for Paired PSCBS
df <- data.frame(chromosome=chromosome, x=x, CT=CT, betaT=betaT,
betaN=betaN);
# Run PSCBS
fit <- segmentByPairedPSCBS(df, verbose=verbose);
print("...segmentByPairedPSCBS")
fit <- callAB(fit, verbose=verbose);
print("...callAB")
fit <- callLOH(fit, verbose=verbose);
print("...callLOH")
===============================================
I wonder if you provide me with any suggestion regarding this error
message.
Thank you,
Best,
Hoon
sessionInfo() is as follows:
===============================================
> sessionInfo()
R version 2.13.0 (2011-04-13)
Platform: x86_64-unknown-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] splines stats graphics grDevices utils datasets
methods
[8] base
other attached packages:
[1] Hmisc_3.8-3 survival_2.36-5 DNAcopy_1.26.0
[4] PSCBS_0.17.1 aroma.affymetrix_2.3.0 affxparser_1.24.0
[7] aroma.apd_0.2.0 R.huge_0.3.0 aroma.core_2.3.2
[10] aroma.light_1.22.0 matrixStats_0.4.3 R.rsp_0.7.0
[13] R.cache_0.5.2 R.filesets_1.1.3 digest_0.5.1
[16] R.utils_1.9.6 R.oo_1.8.3 R.methodsS3_1.2.1
loaded via a namespace (and not attached):
[1] cluster_1.13.3 grid_2.13.0 lattice_0.19-23
===============================================
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