[aroma.affymetrix] No CDF file for chip type found: HuEx-1_0-st-v2

2012-09-12 Thread Maria Rodrigo
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_0.8.2R.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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Re: [aroma.affymetrix] No CDF file for chip type found: HuEx-1_0-st-v2

2012-09-12 Thread Henrik Bengtsson
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_0.8.2R.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.


 You received this message because you are subscribed to the Google Groups
 aroma.affymetrix group with website http://www.aroma-project.org/.
 To post to this group, send email to aroma-affymetrix@googlegroups.com
 To unsubscribe and other options, go to http://www.aroma-project.org/forum/

-- 
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.


You received this message because you are subscribed to the Google Groups 
aroma.affymetrix group with website http://www.aroma-project.org/.
To post to this group, send email to aroma-affymetrix@googlegroups.com
To unsubscribe and other options, go to http://www.aroma-project.org/forum/