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)
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)
Name: GSE7516
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)
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: ",
  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.


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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