Hi, Here is a link to download the files (as a .zip): http://www.yousendit.com/transfer.php?action=batch_download&send_id=64 0189734&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[channelsis.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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> [[alternative HTML version deleted]]