I have figured it out. Some of the annotation files were missing. Found them
and added into the folder and it works now. Thanks.
-Aikseng
On Mon, Aug 22, 2011 at 10:38 AM, Aikseng <aiks...@gmail.com> wrote:
> 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
>
> --
> 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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--
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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