Hi Henrik,
I'm using doASCRMAv2() and then CalMaTe package on a SNP array 6.0 series.
I use the code as found in the vignette of CalMaTeCalibration:
#------------------------------------ # Plot allele B fractions (before and
after) #------------------------------------ # Sample #1 and Chromosome 17
ii <- 1;
# Extract raw (TCN,BAF)
df <- getFile(ds$total, ii);
dfR <- getAverageFile(ds$total, verbose=verbose);
gamma <- extractRawCopyNumbers(df, logBase=NULL, chromosome=chr);
gammaR <- extractRawCopyNumbers(dfR, logBase=NULL, chromosome=chr);
gamma <- 2*divideBy(gamma, gammaR);
All went fine until the yellow-highlighted line, where I got the following
error:
Exception: Failed assign column 'y', because: replacement has 0 rows, data
has 46632
at #07. value[[3L]](cond)
- value[[3L]]() is local of the calling function
at #06. tryCatchOne(expr, names, parentenv, handlers[[1L]])
- tryCatchOne() is local of the calling function
at #05. tryCatchList(expr, classes, parentenv, handlers)
- tryCatchList() is local of the calling function
at #04. tryCatch({
this <- NextMethod("[[<-")
}, error = function(ex) {
msg <- sprintf("Failed assign column '%s', because: %s",
name, ex$message)
throw(msg)
})
- tryCatch() is in environment 'base'
at #03. `[[<-.RichDataFrame`(`*tmp*`, field, value = numeric(0))
- `[[<-.RichDataFrame`() is in environment 'aroma.core'
at #02. `[[<-`(`*tmp*`, field, value = numeric(0))
- `[[<-`() is local of the calling function
at #01. `*.RawGenomicSignals`(2, divideBy(gamma, gammaR))
- `*.RawGenomicSignals`() is in environment 'aroma.core'
Error: Failed assign column 'y', because: replacement has 0 rows, data has
46632
Thanks a lot in advance!
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