Hi,

Here is a link to download the files (as a .zip):
http://www.yousendit.com/transfer.php?action=batch_download&send_id=640189734&email=5f720ea3f2df476bbbbf68766a9fed4a

Strangely, I am able to circumvent the problem by doing

gpr <- GenePixData$read(targets$Filename[1:2], verbose=FALSE)
gpr.2 <- GenePixData$read(targets$Filename[3:4], verbose=FALSE)
# read the 4 first in pairs and append the ladder to to the first 2
append(gpr, gpr.2)

# then read the rest and append one by one
for( k in 5:nrow(targets) ){
	gpr_tmp <- GenePixData$read(targets$Filename[k], verbose=FALSE)
	append(gpr, gpr_tmp)
}


which works but doesn't look very nice.

Thanks
Daniel Klevebring

--

Contact information:

Daniel Klevebring
M. Sc. Eng., Ph.D. Student
Dept of Gene Technology
Royal Institute of Technology, KTH
SE-106 91 Stockholm, Sweden

Visiting address: Roslagstullsbacken 21, B3
Delivery address: Roslagsvägen 30B, 104 06, Stockholm
E-mail: daniel@biotech.kth.se
E-mail: daniel@arrayadvice.se
Phone: +46 8 5537 8337 (Office)
Phone: +46 704 71 65 91 (Mobile)
Web: http://www.biotech.kth.se/genetech/index.html
Web: http://www.arrayadvice.se/
Fax: +46 8 5537 8481
MSN messenger: klevebring@msn.com

On 27 dec 2008, at 15.40, Henrik Bengtsson wrote:

> 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@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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