[BioC] Aroma breaks when reading >2 Agilent 44k custom arrays
Henrik Bengtsson
hb at stat.berkeley.edu
Sat Dec 27 15:40:45 CET 2008
Hi Daniel,
could you please forward an URL where I can download three GPR files
so that I can reproduce the error, and troubleshoot this.
Cheers
/Henrik
On Fri, Dec 19, 2008 at 12:22 PM, Daniel Klevebring
<daniel at biotech.kth.se> wrote:
> Dear list,
>
> I am trying to read a bunch of Agilent custom 44k arrays that have been
> processed with GenePix (i.e. I have .gpr-files).
>
> I am able to read one or two files, but when trying three (any three) it
> breaks giving the following error message:
>
>> gpr <- GenePixData$read(targets$Filename[1:3], verbose=TRUE)
> ...
> Error in paste(channels[channels(is.na(pos))], collapse = ", ") :
> could not find function "channels"
> In addition: Warning messages:
> 1: In readHeader.GenePixData(this, filename = filename, path = NULL, :
> GenePix file format warning: Some of the field names are not recognized. It
> might be because it is a new/old version. The unknown fields are: RefNumber,
> ControlType, GeneName, TopHit, Description.
> 2: In readHeader.GenePixData(this, filename = filename, path = NULL, :
> GenePix file format warning: Some of the field names are not recognized. It
> might be because it is a new/old version. The unknown fields are: RefNumber,
> ControlType, GeneName, TopHit, Description.
> 3: In readHeader.GenePixData(this, filename = filename, path = NULL, :
> GenePix file format warning: Some of the field names are not recognized. It
> might be because it is a new/old version. The unknown fields are: RefNumber,
> ControlType, GeneName, TopHit, Description.
>
>
>
> For convenience, output from the verbose flag is appended to the end of this
> mail. My session info is
>> sessionInfo()
> R version 2.8.0 (2008-10-20)
> i386-apple-darwin8.11.1
>
> locale:
> en_US.UTF-8/en_US.UTF-8/C/C/en_US.UTF-8/en_US.UTF-8
>
> attached base packages:
> [1] stats graphics grDevices utils datasets methods base
> other attached packages:
> [1] aroma_0.94 R.io_0.37 R.graphics_0.42 R.colors_0.5.4
> R.basic_0.49 aroma.light_1.9.2
> [7] R.utils_1.0.9 R.oo_1.4.6 R.methodsS3_1.0.3
>
>
> Any ideas why?
>
> Thanks
> Daniel Klevebring
>
>
>
>
>
>
>
> Output from the verbose=TRUE:
>
> Reading file gprs/252110010002_pmt10_4-4.gpr...Reading the header of file
> gprs/252110010002_pmt10_4-4.gpr...ATF 1.0
> 29 35
> Reading 29 optional header records:
> Type=GenePix Results 3
> DateTime=2008/12/11 10:59:39
> Settings=R:\KTH array\KTH Microarray Production\Gene Expression Service\NEWT
> Matthew Kirkham\NEWT2 pmt10\settings\252110010002_10.gps
> GalFile=R:\KTH array\KTH Microarray Production\Gene Expression Service\NEWT
> Matthew Kirkham\NEWT2.gal
> ArrayOfArrays=4-4
> PixelSize=5
> Wavelengths=532
> ImageFiles=R:\KTH array\KTH Microarray Production\Gene Expression
> Service\NEWT Matthew Kirkham\tiff-files\green
> _252110010002_pmt10_FlippedULtoLR.tif 0
> NormalizationMethod=None
> NormalizationFactors=1
> JpegImage=R:\KTH array\KTH Microarray Production\Gene Expression
> Service\NEWT Matthew Kirkham\NEWT2 pmt10\resultat\252110010002_pmt10.jpg
> StdDev=Type 1
> FeatureType=Irregular Not Filled
> Barcode=NA
> BackgroundSubtraction=LocalFeature
> ImageOrigin=0, 0
> JpegOrigin=800, 1310
> Creator=GenePix Pro 5.1.0.19
> Scanner=G2505B
> FocusPosition=0
> Temperature=0
> LinesAveraged=1
> Comment=NA
> PMTGain=0
> ScanPower=100
> LaserPower=0
> Filters=NA
> ScanRegion=0,0,4320,12200
> Supplier=NA
> Identified channel names: 532, 4, 532, 4
> Header considered to be known: Block, Column, Row, Name, ID, X, Y, Dia\.,
> F532 Median, F532 Mean, F532 SD, B532 Median, B532 Mean, B532 SD, % >
> B532\+1SD, % > B532\+2SD, F532 % Sat\., F4 Median, F4 Mean, F4 SD, B4
> Median, B4 Mean, B4 SD, % > B4\+1SD, % > B4\+2SD, F4 % Sat\., Ratio of
> Medians, Ratio of Means, Median of Ratios, Mean of Ratios, Ratios SD, Rgn
> Ratio, Rgn R, F Pixels, B Pixels, Sum of Medians, Sum of Means, Log Ratio,
> F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean - B4, Flags,
> Normalize, F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean -
> B4, SNR 532, F532 Total Intensity, Index, User Defined, F532 Median, F532
> Mean, F532 SD, B532 Median, B532 Mean, B532 SD, % > B532\+1SD, % >
> B532\+2SD, F532 % Sat\., F4 Median, F4 Mean, F4 SD, B4 Median, B4 Mean, B4
> SD, % > B4\+1SD, % > B4\+2SD, F4 % Sat\., F532 Median - B532, F4 Median -
> B4, F532 Mean - B532, F4 Mean - B4, Ratio of Medians \(532/4\), Ratio of
> Medians \(Ratio/2\), Ratio of Medians \(Ratio/3\), Ratio of Means \(532/4\),
> Ratio of Means \(Ratio/2\), Ratio of Means \(Ratio/3\), Median of Ratios
> \(532/4\), Median of Ratios \(Ratio/2\), Median of Ratios \(Ratio/3\), Mean
> of Ratios \(532/4\), Mean of Ratios \(Ratio/2\), Mean of Ratios \(Ratio/3\),
> Ratios SD \(532/4\), Ratios SD \(Ratio/2\), Ratios SD \(Ratio/3\), Rgn Ratio
> \(532/4\), Rgn Ratio \(Ratio/2\), Rgn Ratio \(Ratio/3\), Rgn R. \(532/4\),
> Rgn R. \(Ratio/2\), Rgn R. \(Ratio/3\), Log Ratio \(532/4\), Log Ratio
> \(Ratio/2\), Log Ratio \(Ratio/3\), Normalize, F532 Total Intensity, F4
> Total Intensity, SNR 532, SNR 4, Negative Control, B532, B4, F4 CV, F532 CV,
> B4 CV, B532 CV, Circularity, Autoflag
> Reading field names...ok
> ok
> Reading result table...45220 lines. ok!
> Successfully read file.
> ok
> Reading file gprs/252110010002_pmt10_3-4.gpr...Reading the header of file
> gprs/252110010002_pmt10_3-4.gpr...ATF 1.0
> 29 35
> Reading 29 optional header records:
> Type=GenePix Results 3
> DateTime=2008/12/11 10:59:39
> Settings=R:\KTH array\KTH Microarray Production\Gene Expression Service\NEWT
> Matthew Kirkham\NEWT2 pmt10\settings\252110010002_10.gps
> GalFile=R:\KTH array\KTH Microarray Production\Gene Expression Service\NEWT
> Matthew Kirkham\NEWT2.gal
> ArrayOfArrays=3-4
> PixelSize=5
> Wavelengths=532
> ImageFiles=R:\KTH array\KTH Microarray Production\Gene Expression
> Service\NEWT Matthew Kirkham\tiff-files\green
> _252110010002_pmt10_FlippedULtoLR.tif 0
> NormalizationMethod=None
> NormalizationFactors=1
> JpegImage=R:\KTH array\KTH Microarray Production\Gene Expression
> Service\NEWT Matthew Kirkham\NEWT2 pmt10\resultat\252110010002_pmt10.jpg
> StdDev=Type 1
> FeatureType=Irregular Not Filled
> Barcode=NA
> BackgroundSubtraction=LocalFeature
> ImageOrigin=0, 0
> JpegOrigin=800, 1310
> Creator=GenePix Pro 5.1.0.19
> Scanner=G2505B
> FocusPosition=0
> Temperature=0
> LinesAveraged=1
> Comment=NA
> PMTGain=0
> ScanPower=100
> LaserPower=0
> Filters=NA
> ScanRegion=0,0,4320,12200
> Supplier=NA
> Identified channel names: 532, 4, 532, 4
> Header considered to be known: Block, Column, Row, Name, ID, X, Y, Dia\.,
> F532 Median, F532 Mean, F532 SD, B532 Median, B532 Mean, B532 SD, % >
> B532\+1SD, % > B532\+2SD, F532 % Sat\., F4 Median, F4 Mean, F4 SD, B4
> Median, B4 Mean, B4 SD, % > B4\+1SD, % > B4\+2SD, F4 % Sat\., Ratio of
> Medians, Ratio of Means, Median of Ratios, Mean of Ratios, Ratios SD, Rgn
> Ratio, Rgn R, F Pixels, B Pixels, Sum of Medians, Sum of Means, Log Ratio,
> F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean - B4, Flags,
> Normalize, F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean -
> B4, SNR 532, F532 Total Intensity, Index, User Defined, F532 Median, F532
> Mean, F532 SD, B532 Median, B532 Mean, B532 SD, % > B532\+1SD, % >
> B532\+2SD, F532 % Sat\., F4 Median, F4 Mean, F4 SD, B4 Median, B4 Mean, B4
> SD, % > B4\+1SD, % > B4\+2SD, F4 % Sat\., F532 Median - B532, F4 Median -
> B4, F532 Mean - B532, F4 Mean - B4, Ratio of Medians \(532/4\), Ratio of
> Medians \(Ratio/2\), Ratio of Medians \(Ratio/3\), Ratio of Means \(532/4\),
> Ratio of Means \(Ratio/2\), Ratio of Means \(Ratio/3\), Median of Ratios
> \(532/4\), Median of Ratios \(Ratio/2\), Median of Ratios \(Ratio/3\), Mean
> of Ratios \(532/4\), Mean of Ratios \(Ratio/2\), Mean of Ratios \(Ratio/3\),
> Ratios SD \(532/4\), Ratios SD \(Ratio/2\), Ratios SD \(Ratio/3\), Rgn Ratio
> \(532/4\), Rgn Ratio \(Ratio/2\), Rgn Ratio \(Ratio/3\), Rgn R. \(532/4\),
> Rgn R. \(Ratio/2\), Rgn R. \(Ratio/3\), Log Ratio \(532/4\), Log Ratio
> \(Ratio/2\), Log Ratio \(Ratio/3\), Normalize, F532 Total Intensity, F4
> Total Intensity, SNR 532, SNR 4, Negative Control, B532, B4, F4 CV, F532 CV,
> B4 CV, B532 CV, Circularity, Autoflag
> Reading field names...ok
> ok
> Reading result table...45220 lines. ok!
> Successfully read file.
> ok
> Reading file gprs/252110010002_pmt10_2-4.gpr...Reading the header of file
> gprs/252110010002_pmt10_2-4.gpr...ATF 1.0
> 29 35
> Reading 29 optional header records:
> Type=GenePix Results 3
> DateTime=2008/12/11 10:59:39
> Settings=R:\KTH array\KTH Microarray Production\Gene Expression Service\NEWT
> Matthew Kirkham\NEWT2 pmt10\settings\252110010002_10.gps
> GalFile=R:\KTH array\KTH Microarray Production\Gene Expression Service\NEWT
> Matthew Kirkham\NEWT2.gal
> ArrayOfArrays=2-4
> PixelSize=5
> Wavelengths=532
> ImageFiles=R:\KTH array\KTH Microarray Production\Gene Expression
> Service\NEWT Matthew Kirkham\tiff-files\green
> _252110010002_pmt10_FlippedULtoLR.tif 0
> NormalizationMethod=None
> NormalizationFactors=1
> JpegImage=R:\KTH array\KTH Microarray Production\Gene Expression
> Service\NEWT Matthew Kirkham\NEWT2 pmt10\resultat\252110010002_pmt10.jpg
> StdDev=Type 1
> FeatureType=Irregular Not Filled
> Barcode=NA
> BackgroundSubtraction=LocalFeature
> ImageOrigin=0, 0
> JpegOrigin=800, 1310
> Creator=GenePix Pro 5.1.0.19
> Scanner=G2505B
> FocusPosition=0
> Temperature=0
> LinesAveraged=1
> Comment=NA
> PMTGain=0
> ScanPower=100
> LaserPower=0
> Filters=NA
> ScanRegion=0,0,4320,12200
> Supplier=NA
> Identified channel names: 532, 4, 532, 4
> Header considered to be known: Block, Column, Row, Name, ID, X, Y, Dia\.,
> F532 Median, F532 Mean, F532 SD, B532 Median, B532 Mean, B532 SD, % >
> B532\+1SD, % > B532\+2SD, F532 % Sat\., F4 Median, F4 Mean, F4 SD, B4
> Median, B4 Mean, B4 SD, % > B4\+1SD, % > B4\+2SD, F4 % Sat\., Ratio of
> Medians, Ratio of Means, Median of Ratios, Mean of Ratios, Ratios SD, Rgn
> Ratio, Rgn R, F Pixels, B Pixels, Sum of Medians, Sum of Means, Log Ratio,
> F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean - B4, Flags,
> Normalize, F532 Median - B532, F4 Median - B4, F532 Mean - B532, F4 Mean -
> B4, SNR 532, F532 Total Intensity, Index, User Defined, F532 Median, F532
> Mean, F532 SD, B532 Median, B532 Mean, B532 SD, % > B532\+1SD, % >
> B532\+2SD, F532 % Sat\., F4 Median, F4 Mean, F4 SD, B4 Median, B4 Mean, B4
> SD, % > B4\+1SD, % > B4\+2SD, F4 % Sat\., F532 Median - B532, F4 Median -
> B4, F532 Mean - B532, F4 Mean - B4, Ratio of Medians \(532/4\), Ratio of
> Medians \(Ratio/2\), Ratio of Medians \(Ratio/3\), Ratio of Means \(532/4\),
> Ratio of Means \(Ratio/2\), Ratio of Means \(Ratio/3\), Median of Ratios
> \(532/4\), Median of Ratios \(Ratio/2\), Median of Ratios \(Ratio/3\), Mean
> of Ratios \(532/4\), Mean of Ratios \(Ratio/2\), Mean of Ratios \(Ratio/3\),
> Ratios SD \(532/4\), Ratios SD \(Ratio/2\), Ratios SD \(Ratio/3\), Rgn Ratio
> \(532/4\), Rgn Ratio \(Ratio/2\), Rgn Ratio \(Ratio/3\), Rgn R. \(532/4\),
> Rgn R. \(Ratio/2\), Rgn R. \(Ratio/3\), Log Ratio \(532/4\), Log Ratio
> \(Ratio/2\), Log Ratio \(Ratio/3\), Normalize, F532 Total Intensity, F4
> Total Intensity, SNR 532, SNR 4, Negative Control, B532, B4, F4 CV, F532 CV,
> B4 CV, B532 CV, Circularity, Autoflag
> Reading field names...ok
> ok
> Reading result table...45220 lines. ok!
> Successfully read file.
> ok
>
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