Hi.
The rather confusing error message actually implies that no data files
where found in the data set directory. So:
1. Make sure you have your CEL files in rawData/B&T/Mapping250K_Nsp/
2. Does print(list.files(path=getPath(csR)) list your CEL files?
3. See troubleshooting page on 'Setup of directory structures':
http://aroma-project.org/troubleshooting/DirectoryStructures
4. Update aroma.affymetrix to v1.9.0, cf. http://aroma-project.org/install
5. Try csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf,
verbose=-10); It should show how many files it finds.
BTW, although
cdf <- AffymetrixCdfFile$byName(chipType);
happens to work (and not the cause of your problems), you should really use
cdf <- AffymetrixCdfFile$byChipType(chipType);
Let us know if any of these helped.
/Henrik
On Fri, Feb 4, 2011 at 6:16 AM, Sake van Pelt <tlep.nav.eka...@gmail.com> wrote:
> Hi All,
>
> I´m encountering a problem with the following code:
>
>
>>library("aroma.affymetrix");
>>library("ACNE");
>>log <- verbose <- Arguments$getVerbose(-8, timestamp=TRUE);
>
>>setwd("D:/Users/Who Am I/Documents/0School/Jaar 5/BMCG/Array data/LUMC SNP
>>250k nsp");
>
>>dataSetName <- "B&T";
>>chipType <- "Mapping250K_Nsp";
>
>>pairs <- matrix(c(
>
> "AR1000900A_N_241110_(Mapping250K_Nsp)_2.CEL","AR1000900B_N_241110_(Mapping250K_Nsp)_2.CEL",
>
> "AR1000901A_N_241110_(Mapping250K_Nsp).CEL","AR1000901B_N_241110_(Mapping250K_Nsp).CEL",
>
> "AR1000902A_N_241110_(Mapping250K_Nsp).CEL","AR1000902B_N_241110_(Mapping250K_Nsp).CEL",
>
> "AR1000903A_N_291110_(Mapping250K_Nsp).CEL","AR1000903B_N_241110_(Mapping250K_Nsp).CEL",
>
> "AR1000904A_N_241110_(Mapping250K_Nsp).CEL","AR1000904B_N_241110_(Mapping250K_Nsp).CEL"
> ), ncol=2, byrow=TRUE);
>>colnames(pairs) <- c("Tumor", "Bloed");
>
>>cdf <- AffymetrixCdfFile$byName(chipType);
>>csR <- AffymetrixCelSet$byName(dataSetName, cdf=cdf);
>>print(csR);
>
> Error in list(`print(csR)` = <environment>, `print.Object(csR)` =
> <environment>, :
>
> [2011-02-04 15:04:48] Exception: Argument 'x' is of length 1 although
> the range ([0,0]) implies that is should be empty.
> at throw(Exception(...))
> at throw.default(sprintf("Argument 'x' is of length %d although the
> range ([%s,%s]) implies that is should be empty.", length(x),
> range[1], range[2]))
> at throw(sprintf("Argument 'x' is of length %d although the range
> ([%s,%s]) implies that is should be empty.", length(x), range[1],
> range[2]))
> at getIndices.Arguments(static, ..., length = length)
> at getIndices(static, ..., length = length)
> at method(static, ...)
> at Arguments$getIndex(idx, max = n)
> at getFile.GenericDataFileSet(this, 1)
> at getFile(this, 1)
> at getUnitNamesFile.AffymetrixCelSet(this)
> at getUnitNamesFile(this)
> at getChipType.AffymetrixCelSet(this)
> at getChipType(this)
> at sprintf("Chip type: %s", getChipType(this))
> at as.character.AffymetrixCelSet(x)
> at as.character(x)
> at print(as.character(x))
> at print.Object(csR)
> at print(csR)
>
>> sessionInfo()
> R version 2.12.1 (2010-12-16)
> Platform: x86_64-pc-mingw32/x64 (64-bit)
>
> locale:
> [1] LC_COLLATE=Dutch_Netherlands.1252 LC_CTYPE=Dutch_Netherlands.
> 1252 LC_MONETARY=Dutch_Netherlands.1252
> LC_NUMERIC=C
> [5] LC_TIME=Dutch_Netherlands.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] ACNE_0.4.2 MASS_7.3-9
> aroma.affymetrix_1.7.0 aroma.apd_0.1.7 affxparser_1.20.0
> R.huge_0.2.0 aroma.core_1.7.0
> [8] aroma.light_1.16.1 matrixStats_0.2.2
> R.rsp_0.4.0 R.cache_0.3.0 R.filesets_0.9.0
> digest_0.4.2 R.utils_1.5.3
> [15] R.oo_1.7.4 R.methodsS3_1.2.1
>
>
>> traceback()
> 20: throw.Exception(Exception(...))
> 19: throw(Exception(...))
> 18: throw.default(sprintf("Argument 'x' is of length %d although the
> range ([%s,%s]) implies that is should be empty.",
> length(x), range[1], range[2]))
> 17: throw(sprintf("Argument 'x' is of length %d although the range
> ([%s,%s]) implies that is should be empty.",
> length(x), range[1], range[2]))
> 16: getIndices.Arguments(static, ..., length = length)
> 15: getIndices(static, ..., length = length)
> 14: method(static, ...)
> 13: Arguments$getIndex(idx, max = n)
> 12: getFile.GenericDataFileSet(this, 1)
> 11: getFile(this, 1)
> 10: getUnitNamesFile.AffymetrixCelSet(this)
> 9: getUnitNamesFile(this)
> 8: getChipType.AffymetrixCelSet(this)
> 7: getChipType(this)
> 6: sprintf("Chip type: %s", getChipType(this))
> 5: as.character.AffymetrixCelSet(x)
> 4: as.character(x)
> 3: print(as.character(x))
> 2: print.Object(csR)
> 1: print(csR)
>
> All the .CEL files and the .cdf annotation file are in the right path
> as described at http://www.aroma-project.org/node/68 and
> http://aroma-project.org/node/66.
>
> --
> When reporting problems on aroma.affymetrix, make sure 1) to run the latest
> version of the package, 2) to report the output of sessionInfo() and
> traceback(), and 3) to post a complete code example.
>
>
> You received this message because you are subscribed to the Google Groups
> "aroma.affymetrix" group with website http://www.aroma-project.org/.
> To post to this group, send email to aroma-affymetrix@googlegroups.com
> To unsubscribe and other options, go to http://www.aroma-project.org/forum/
>
--
When reporting problems on aroma.affymetrix, make sure 1) to run the latest
version of the package, 2) to report the output of sessionInfo() and
traceback(), and 3) to post a complete code example.
You received this message because you are subscribed to the Google Groups
"aroma.affymetrix" group with website http://www.aroma-project.org/.
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