CalMaTe running error with function "divideBy"

[Qingyao Huang]

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!