Hi.
On Wed, Sep 12, 2012 at 6:07 AM, Maria Rodrigo <mrod...@gmail.com> wrote:
> Hi,
>
> I have come across an error when extracting probe intensities from the exon
> array using function getUnitIntensities()
>
> "Error in readCelUnits(pathnames, cdf = cdfUnits, readStdvs = FALSE,
> readPixels = FALSE, :
> No CDF file for chip type found: HuEx-1_0-st-v2"
>
> I found the same error in the google group archive, but for another array
> (GenomeWideSNP_6), and I didn't find a solution for the problem.
>
> I have used getUnitIntensities() many times before and I never had this
> problem. I found another function that does work: readUnits(), but do they
> extract the same estimates?
Yes, by default they do, so use readUnits() instead.
Also, readUnits() [and getUnitIntensities()] are actually by default
caching the results in memory, which you often don't want, especially
for large data sets, so do:
data <- readUnits(csN, cache=FALSE)
FYI, there was a "bug" in getUnitIntensities() causing your problems,
which is now corrected.
/Henrik
>
> I have pasted the code below.
>
> Thank you for your help!
> Best,
> Maria Rodrigo-Domingo
> PhD student - Biostatistics
> Aalborg Hospital Science and Innovation Center
> Department of Haematology
> Aarhus University Hospital
> Sdr. Skovvej 15
> DK-9000 Aalborg
> DENMARK
>
> This is my code:
>> ds <- "AffyColonCancer"
>> chipType <- "HuEx-1_0-st-v2"
>> cdf <- AffymetrixCdfFile$byChipType(
> chipType,
> + tags = "coreR3,A20071112,EP")
>> cs <- AffymetrixCelSet$byName(ds, cdf = cdf)
>> cs
> AffymetrixCelSet:
> Name: AffyColonCancer
> Tags:
> Path: rawData/AffyColonCancer/HuEx-1_0-st-v2
> Platform: Affymetrix
> Chip type: HuEx-1_0-st-v2,coreR3,A20071112,EP
> Number of arrays: 20
> Names: 1_1T, 10_5N, 11_6T, ..., 9_5T [20]
> Time period: 2005-05-25 14:01:47 -- 2005-05-26 07:49:40
> Total file size: 1271.67MB
> RAM: 0.02MB
>> bc <- RmaBackgroundCorrection(cs)
>> csBC <- process(bc, verbose = verbose)
> Background correcting data set...
> Already background corrected
> Background correcting data set...done
>> qn <- QuantileNormalization(csBC,
> + typesToUpdate = "pm")
>> csN <- process(qn, verbose = verbose)
> Quantile normalizing data set...
> Already normalized
> Quantile normalizing data set...done
>> read.units <- readUnits(csN)
>> get.intensities <- getUnitIntensities(csN)
> Error in readCelUnits(pathnames, cdf = cdfUnits, readStdvs = FALSE,
> readPixels = FALSE, :
> No CDF file for chip type found: HuEx-1_0-st-v2
>
>> sessionInfo()
> R version 2.15.1 (2012-06-22)
> Platform: i386-pc-mingw32/i386 (32-bit)
>
> locale:
> [1] LC_COLLATE=Danish_Denmark.1252 LC_CTYPE=Danish_Denmark.1252
> [3] LC_MONETARY=Danish_Denmark.1252 LC_NUMERIC=C
> [5] LC_TIME=Danish_Denmark.1252
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
>
> other attached packages:
> [1] aroma.affymetrix_2.5.0 affxparser_1.28.1 aroma.apd_0.2.3
> [4] R.huge_0.4.1 aroma.core_2.5.0 aroma.light_1.24.0
> [7] matrixStats_0.5.2 R.rsp_0.8.2 R.devices_2.1.1
> [10] R.cache_0.6.2 R.filesets_1.1.5 digest_0.5.2
> [13] R.utils_1.12.1 R.oo_1.9.8 R.methodsS3_1.4.2
>
>> traceback()
> 4: stop("No CDF file for chip type found: ", chipType)
> 3: readCelUnits(pathnames, cdf = cdfUnits, readStdvs = FALSE, readPixels =
> FALSE,
> dropArrayDim = FALSE, ...)
> 2: getUnitIntensities.AffymetrixCelSet(csN)
> 1: getUnitIntensities(csN)
>
> --
> 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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