Hi,
I am new to aroma.affymetrix. I am trying to use it to read in ChIP on
Chip data, and encounter the following problem.
> cdfT <- AffymetrixCdfFile$byChipType("Hs_PromPR_v02")
> print(cdfT)
AffymetrixCdfFile:
Path: annotationData/chipTypes/Hs_PromPR_v02
Filename: Hs_PromPR_v02.cdf
Filesize: 61.95MB
Chip type: Hs_PromPR_v02
RAM: 0.00MB
File format: v4 (binary; XDA)
Dimension: 2166x2166
Number of cells: 4691556
Number of units: 23155
Cells per unit: 202.62
Number of QC units: 0
> csT <- AffymetrixCelSet$byName("GSE7516", cdf = cdfT)
> print(csT)
AffymetrixCelSet:
Name: GSE7516
Tags:
Path: rawData/GSE7516/Hs_PromPR_v02
Platform: Affymetrix
Chip type: Hs_PromPR_v02
Number of arrays: 30
Names: GSM182106, GSM182107, GSM182108, ..., GSM182135 [30]
Time period: 2006-06-01 14:22:27 -- 2006-10-26 18:48:30
Total file size: 1347.84MB
RAM: 0.03MB
> MN <- MatNormalization(csT)
> print(MN)
MatNormalization:
Data set: GSE7516
Input tags:
User tags: *
Asterisk ('*') tags: MN,lm
Output tags: MN,lm
Number of files: 30 (1347.84MB)
Platform: Affymetrix
Chip type: Hs_PromPR_v02
Algorithm parameters: (unitsToFit: NULL, typesToFit: chr "pm",
unitsToUpdate: NULL, typesToUpdate: chr "pm", shift: num 0, target:
NULL, model: chr "lm", nbrOfBins: int 200)
Output path: probeData/GSE7516,MN,lm/Hs_PromPR_v02
Is done: FALSE
RAM: 0.00MB
> csTMN <- process(MN, verbose=verbose)
Normalization data set for probe-sequence effects...
Locating probe-sequence annotation data...
Error in list(`process(MN, verbose = verbose)` = <environment>,
`process.MatNormalization(MN, verbose = verbose)` = <environment>, :
[2011-08-22 10:26:14] Exception: Could not locate a file for this chip
type: Hs_PromPR_v02
at throw(Exception(...))
at throw.default("Could not locate a file for this chip type: ",
paste(c(chipT
at throw("Could not locate a file for this chip type: ",
paste(c(chipType, tag
at method(static, ...)
at AromaCellSequenceFile$byChipType(chipType, nbrOfCells =
nbrOfCells, ..., ve
at getAromaCellSequenceFile.AbstractProbeSequenceNormalization(this,
verbose =
at getAromaCellSequenceFile(this, verbose = less(verbose, 5))
at process.MatNormalization(MN, verbose = verbose)
at process(MN, verbose = verbose)
Locating probe-sequence annotation data...done
Normalization data set for probe-sequence effects...done
Any help is much appreciated. Thank you.
-Aikseng
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