Hi Carol.
This is very strange indeed. A couple thoughts come to mind:
i) are there filenames in the directory (rawData/MGH09/MoGene-1_0-st-
v1) that have strange characters?
ii) are there other R packages loaded that may have a clash?
To test, maybe delete your existing "probeData/MGH09,RBC/MoGene-1_0-st-
v1" directory, make sure you are running a fresh R session and check
the filenames ...
Cheers,
Mark
On 15-Oct-09, at 1:25 AM, cjb wrote:
>
> Hi Pierre,
>
> I did change the command to create the cs object, but I"m still
> getting the error message.
>
> Error and sessionInfo() info is below...
>
> Thanks much,
>
> Carol
>
>> cdf <- AffymetrixCdfFile$byChipType("MoGene-1_0-st-v1")
>> cs <- AffymetrixCelSet$byName("MGH09", cdf=cdf)
>> bc <- RmaBackgroundCorrection(cs)
>> csBC <- process(bc, verbose=verbose)
> Background correcting data set...
> Error in list(`process(bc, verbose = verbose)` = <environment>,
> `process.RmaBackgroundCorrection(bc, verbose = verbose)` =
> <environment>, :
>
> [2009-10-14 10:20:19] Exception: Unknown arguments: cdf, checkChipType
> at throw(Exception(...))
> at throw.default("Unknown arguments: ", argsStr)
> at throw("Unknown arguments: ", argsStr)
> at GenericDataFileSet(files = files, ...)
> at extend(GenericDataFileSet(files = files, ...),
> "AromaMicroarrayDataSet")
> at AromaMicroarrayDataSet(files = files, ...)
> at extend(AromaMicroarrayDataSet(files = files, ...), c
> ("AffymetrixFileSet", u
> at AffymetrixFileSet(files = files, ...)
> at extend(AffymetrixFileSet(files = files, ...), "AffymetrixCelSet",
> `cached:.
> at this(...)
> at newInstance.Class(clazz, ...)
> at newInstance(clazz, ...)
> at newInstance.Object(static, files, ...)
> at newInstance(static, files, ...)
> at method(static, ...)
> at staticMethod(path = "probeData/MGH09,RBC/MoGene-1_0-st-v1",
> pattern = "^[^.
> at do.call("staticMethod", args = args)
> at getOutputDataSet0.AromaTransform(this, ..., verbose = less
> (verbose, 10))
> at getOutputDataSet0(this, ..., ve
> Background correcting data set...done
>> sessionInfo()
> R version 2.9.2 (2009-08-24)
> i386-pc-mingw32
>
> locale:
> LC_COLLATE=English_United States.1252;LC_CTYPE=English_United States.
> 1252;LC_MONETARY=English_United States.
> 1252;LC_NUMERIC=C;LC_TIME=English_United States.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods
> base
>
> other attached packages:
> [1] abind_1.1-0 aroma.affymetrix_1.2.0
> aroma.apd_0.1.6
> [4] affxparser_1.16.0 R.huge_0.1.9
> aroma.core_1.2.1
> [7] aroma.light_1.12.2 matrixStats_0.1.4
> R.rsp_0.3.6
> [10] R.filesets_0.6.0 digest_0.4.1
> R.cache_0.1.9
> [13] R.utils_1.2.1 R.oo_1.6.0
> EBImage_3.0.5
> [16] R.methodsS3_1.0.3
>>
>
>
> Carol
>
>
> On Oct 13, 12:50 am, Pierre Neuvial <pie...@stat.berkeley.edu> wrote:
>> Hi Carol,
>>
>>
>>
>> On Mon, Oct 12, 2009 at 9:15 AM, cjb <carol.b...@gmail.com> wrote:
>>
>>> Hi all,
>>
>>> I am following along with the Gene 1.0 ST Vignette:
>>> http://groups.google.com/group/aroma-affymetrix/web/gene-1-0-st-array
>>> ...
>>
>>> and with Henrik's August 7, 2007 aroma.affymetrix tutorial.
>>
>>> All goes well until I try to do background correction or quantile
>>> normalization.
>>
>>> When I try to do either background correction or quantile
>>> normalization I get a similar error:
>>> Exception: Unknown arguments: cdf, checkChipType
>>
>>> When I look in my working directory, there is a probeData directory
>>> that has been created. And within that directory, two directories
>>> with
>>> tags.
>>
>>> MGH_Data\probeData\MGH09,QN\MoGene-1_0-st-v1
>>
>>> MGH_Data\probeData\MGH09,RBC\MoGene-1_0-st-v1
>>
>>> 1. Creating the cdf and cs objects:
>>
>>>> cdf <- AffymetrixCdfFile$byChipType("MoGene-1_0-st-v1")
>>>> cdf
>>> AffymetrixCdfFile:
>>> Path: annotationData/chipTypes/MoGene-1_0-st-v1
>>> Filename: MoGene-1_0-st-v1.cdf
>>> Filesize: 67.42MB
>>> Chip type: MoGene-1_0-st-v1
>>> RAM: 0.00MB
>>> File format: v3 (text; ASCII)
>>> Dimension: 1050x1050
>>> Number of cells: 1102500
>>> Number of units: 35512
>>> Cells per unit: 31.05
>>> Number of QC units: 1
>>
>>>> cs <- AffymetrixCelSet$byName("MGH09",chipType="MoGene-1_0-st-v1")
>>>> print(cs)
>>> AffymetrixCelSet:
>>> Name: MGH09
>>> Tags:
>>> Path: rawData/MGH09/MoGene-1_0-st-v1
>>> Platform: Affymetrix
>>> Chip type: MoGene-1_0-st-v1
>>> Number of arrays: 26
>>> Names: J001_3_11.5, J001_4_11.5, ..., J010_4_16.5
>>> Time period: 2009-09-23 17:51:49 -- 2009-09-23 21:45:31
>>> Total file size: 275.06MB
>>> RAM: 0.02MB
>>
>> Have you tried
>>
>> cs <- AffymetrixCelSet$byName("MGH09", cdf=cdf)
>>
>> instead, as in the Gene 1.0 ST Vignette you are citing ?
>>
>> Also, are you using the latest versions of the packages ? Please give
>> the output of sessionInfo() so that we can figure this out.
>>
>> Best,
>>
>> Pierre.
>>
>>> 2. RmaBackgroundCorrection(s) Error:
>>
>>>> bc <- RmaBackgroundCorrection(cs)
>>>> csBC <- process(bc, verbose=verbose)
>>> Background correcting data set...
>>
>>> Error in list(`process(bc, verbose = verbose)` = <environment>,
>>> `process.RmaBackgroundCorrection(bc, verbose = verbose)` =
>>> <environment>, :
>>
>>> [2009-10-12 11:49:04] Exception: Unknown arguments: cdf,
>>> checkChipType
>>> at throw(Exception(...))
>>> at throw.default("Unknown arguments: ", argsStr)
>>> at throw("Unknown arguments: ", argsStr)
>>> at GenericDataFileSet(files = files, ...)
>>> at extend(GenericDataFileSet(files = files, ...),
>>> "AromaMicroarrayDataSet")
>>> at AromaMicroarrayDataSet(files = files, ...)
>>> at extend(AromaMicroarrayDataSet(files = files, ...), c
>>> ("AffymetrixFileSet", uses("AromaPlatformI
>>> at AffymetrixFileSet(files = files, ...)
>>> at extend(AffymetrixFileSet(files = files, ...),
>>> "AffymetrixCelSet",
>>> `cached:.intensities` = NULL
>>> at this(...)
>>> at newInstance.Class(clazz, ...)
>>> at newInstance(clazz, ...)
>>> at newInstance.Object(static, files, ...)
>>> at newInstance(static, files, ...)
>>> at method(static, ...)
>>> at staticMethod(path = "probeData/MGH09,RBC/MoGene-1_0-st-v1",
>>> pattern = "^[^.].*[.](CEL|cel)$",
>>> at do.call("staticMethod", args = args)
>>> at getOutputDataSet0.AromaTransform(this, ..., verbose
>>> Background correcting data set...done
>>
>>> 3. QuantileNormalization(cs) Error:
>>
>>>> qn <-QuantileNormalization(cs)
>>>> qn
>>> Error in list(`print(NA)` = <environment>, `print.Object(NA)` =
>>> <environment>, :
>>
>>> [2009-10-12 11:33:42] Exception: Unknown arguments: cdf,
>>> checkChipType
>>> at throw(Exception(...))
>>> at throw.default("Unknown arguments: ", argsStr)
>>> at throw("Unknown arguments: ", argsStr)
>>> at GenericDataFileSet(files = files, ...)
>>> at extend(GenericDataFileSet(files = files, ...),
>>> "AromaMicroarrayDataSet")
>>> at AromaMicroarrayDataSet(files = files, ...)
>>> at extend(AromaMicroarrayDataSet(files = files, ...), c
>>> ("AffymetrixFileSet", u
>>> at AffymetrixFileSet(files = files, ...)
>>> at extend(AffymetrixFileSet(files = files, ...),
>>> "AffymetrixCelSet",
>>> `cached:.
>>> at this(...)
>>> at newInstance.Class(clazz, ...)
>>> at newInstance(clazz, ...)
>>> at newInstance.Object(static, files, ...)
>>> at newInstance(static, files, ...)
>>> at method(static, ...)
>>> at staticMethod(path = "probeData/MGH09,QN/MoGene-1_0-st-v1",
>>> pattern = "^[^.]
>>> at do.call("staticMethod", args = args)
>>
>>
> >
------------------------------
Mark Robinson, PhD (Melb)
Epigenetics Laboratory, Garvan
Bioinformatics Division, WEHI
e: m.robin...@garvan.org.au
e: mrobin...@wehi.edu.au
p: +61 (0)3 9345 2628
f: +61 (0)3 9347 0852
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