[aroma.affymetrix] Exporting B-allele Frequencies and Log R ratios

[Marijana Vujkovic]

Hello,

I am having some troubles with exporting my data from CEL files to B-allele 
Frequency Files and Log R Ratios. I have successfully installed the aroma 
packages, made the appropriate directories for annotationData and rawData, 
and so far there are some basic setting statements that work fine. 

library('aroma.affymetrix')
library("aroma.core")
tags <- "ACC,ra,-XY,BPN,-XY,AVG,A+B,FLN,-XY";
dataSet <- "AAML0531";
chipType <- "GenomeWideSNP_6";

# call annotation file
cdf <- AffymetrixCdfFile$byChipType(chipType=chipType)
csRone <- AffymetrixCelSet$byName(dataSet, cdf=cdf);

This works fine.. Then I saw the export manual on the website, and 
following the http://www.aroma-project.org/howtos/writeDataFrame and I get 
the following error message when I try to set up the following. 

# set the workin directory and dataset
ds <- AromaUnitTotalCnBinarySet$byName(dataSet, tags=tags, 
chipType=chipType);

Could you please help me resolving this issue? Thanks so much,

Marijana

Error message
[2013-05-28 18:15:23] Exception: No such root path directories:

  at #09. findByName.GenericDataFileSet(static, name = name, tags = tags,
              chipType = chipType, ..., paths = paths, mustExist = TRUE,
              subdirs = "GenomeWideSNP_6")
          - findByName.GenericDataFileSet() is in environment 'R.filesets'

  at #08. NextMethod("findByName", subdirs = chipType)
          - NextMethod() is in environment 'base'

  at #07. findByName.AromaUnitSignalBinarySet(static, name = name, tags = 
tags,
              chipType = chipType, ..., paths = paths, mustExist = TRUE)
          - findByName.AromaUnitSignalBinarySet() is in environment 
'aroma.core'

  at #06. findByName(static, name = name, tags = tags, chipType = chipType,
              ..., paths = paths, mustExist = TRUE)
          - findByName() is in environment 'R.filesets'

  at #05. withCallingHandlers(expr, warning = function(w) 
invokeRestart("muffleWarning"))
          - withCallingHandlers() is in environment 'base'

  at #04. suppressWarnings({
              path <- findByName(static, name = name, tags = tags, chipType 
= chipType,
                  ..., paths = paths, mustExist = TRUE)
          })
          - suppressWarnings() is in environment 'base'

  at #03. byName.AromaUnitTotalCnBinarySet(static, ...)
          - byName.AromaUnitTotalCnBinarySet() is in environment 
'aroma.core'

  at #02. byName(static, ...)
          - byName() is in environment 'R.filesets'
          - originating from '<text>'

  at #01. AromaUnitTotalCnBinarySet$byName(dataSet, tags = tags, chipType = 
chipType)
          - AromaUnitTotalCnBinarySet$byName() is local of the calling 
function

Error: No such root path directories:



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