[BioC] Aroma breaks when reading >2 Agilent 44k custom arrays
Daniel Klevebring
daniel at biotech.kth.se
Fri Dec 19 12:22:39 CET 2008
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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