Hi Minya,
what does sessionInfo() report after library("PSCBS")?
Also, could you please send me (offline; not to the mailinglist) the
following 'MP20120106.Rbin' file:
> df <- data.frame(chromosome=chromosome, x=x, CT=CT, betaT=betaT,
betaN=betaN);
> saveObject(df, "MP20120106.Rbin");
/Henrik
On Friday, January 6, 2012, Minya Pu wrote:
> 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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