[aroma.affymetrix] CalMaTe running error with function "divideBy"

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[aroma.affymetrix] 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!


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