Hi,
I am doing paired PSCBS analysis on a Genome Wide SNP array 6.0 data set.
Following the code on the aroma web site, among 11 pairs of the samples
from, I have successfully done the analysis for 10 of them but got stuck in
one.
Below is the error message from the 'bad' pair, it came out at the
segmentByPairedPSCBS step:
startRow endRow
1 1 3876
2 3877 8743
3 8744 11707
4 11708 11901
5 11902 13071
6 13072 13474
7 13475 14880
8 14881 16114
9 16115 21428
10 21429 21466
11 21467 23886
12 23887 24009
13 24010 35079
startRow endRow
1 25 3853
2 3896 8716
3 8762 11707
4 11710 11897
5 11909 13068
6 13075 13441
7 13492 14874
8 14883 16113
9 16116 21428
10 21430 21465
11 21469 23879
12 23890 23988
13 24028 35025
20120105 16:43:25| Number of TCNs before: 35078
20120105 16:43:25| Number of TCNs after: 35079
20120105 16:43:25| TCN segment #1 ('1') of 5...done
20120105 16:43:25| TCN segment #2 ('2') of 5...
20120105 16:43:25| Nothing todo. Only one DH segmentation. Skipping.
20120105 16:43:25| TCN segment #2 ('2') of 5...done
20120105 16:43:25| TCN segment #3 ('3') of 5...
20120105 16:43:25| Nothing todo. Only one DH segmentation. Skipping.
20120105 16:43:25| TCN segment #3 ('3') of 5...done
20120105 16:43:25| TCN segment #4 ('4') of 5...
20120105 16:43:25| Nothing todo. Only one DH segmentation. Skipping.
20120105 16:43:25| TCN segment #4 ('4') of 5...done
20120105 16:43:25| TCN segment #5 ('5') of 5...
20120105 16:43:25| Nothing todo. Only one DH segmentation. Skipping.
20120105 16:43:25| TCN segment #5 ('5') of 5...done
Error: all(tcnSegRowsCC[-nrow(tcnSegRowsCC), 2] < tcnSegRowsCC[-1, 1], ....
is not TRUE
Any suggestion on what might go wrong?
Below is the code I used.
Thanks so much,
Minya
library("PSCBS");
for (i in 1:11 ){
# Extract tumor-normal pair of interest
pair <- c(T=tumors[i], N=normals[i]);
csR2 <- extract(csR, indexOf(csR, pair));
print(csR2);
res <- doASCRMAv2(csR2, verbose=verbose);
data <- extractPSCNArray(res$total);
dimnames(data)[[3]] <- names(pair);
str(data);
# Total CNs for the tumor relative to the matched normal
CT <- 2 * (data[,"total","T"] / data[,"total","N"]);
# Allele B fractions for the tumor
betaT <- data[,"fracB","T"];
# Allele B fractions for the normal
betaN <- data[,"fracB","N"];
ugp <- getAromaUgpFile(res$total);
chromosome <- ugp[,1,drop=TRUE];
x <- ugp[,2,drop=TRUE];
### x is position ###
df <- data.frame(chromosome=chromosome, x=x, CT=CT, betaT=betaT,
betaN=betaN);
fit1 <- segmentByPairedPSCBS(df, verbose=verbose);
segs <- getSegments(fit1);
print(segs);
pairName =paste(pair, collapse="vs");
chrTag <- sprintf("Chr%s", seqToHumanReadable(getChromosomes(fit1)));
toPNG(pairName, tags=c(chrTag, "PairedPSCBS"), width=840, aspectRatio=0.6, {
plotTracks(fit1);
});
}
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