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-analysis
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
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)
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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.
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