Hi, I managed to fix my problem. So please disregard the previous post.
Marijana
On Tuesday, May 28, 2013 6:19:55 PM UTC-4, Marijana Vujkovic wrote:
>
> 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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