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?
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)
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