Been handed a bunch of gpr files this with a two day limit to do the analysis. The problem is that I can not get LIMMA to read the gpr files. Anyone run into this problem ? I have checked the gpr file format and this seems compliant, Yet rg <- read.maimages(files=targets$FileName[1], source='genepix') Error in sub("^\"", "", readLines(con, n = 1)) : input string 1 is invalid in this locale Is this the ATF value ? Chris """ header plus one row """ ATF 1.0 30 56 "Type=GenePix Results 3" "DateTime=2009/12/05 13:29:02" "Settings=" "GalFile=C:\Hilde Sunniva\SunnivaLitRh?st2009\vibrio_v1.0.2.gal" "PixelSize=10" "Wavelengths=635 532" "ImageFiles=C:\Hilde Sunniva\SunnivaLitRhost2009 \2009-12-05_AA_Cy3_hODwt3_Cy5_hODLitR3_12ug_vibrio slide 339709_1 line_Ometning.tif2 C:\Hilde Sunniva\SunnivaLitRhost2009 \2009-12-05_AA_Cy3_hODwt3_Cy5_hODLitR3_12 ug_vibrio slide 339709_1line_Ometning.tif3" "NormalizationMethod=None" "NormalizationFactors=1 1" "JpegImage=C:\HildeSunniva\SunnivaLitRhost2009 \2009-12-05_AA_Cy3_hODwt3_Cy5_hODLitR3_12ug_vibrioslide 339709.jpg" "StdDev=Type 1" "RatioFormulations=W1/W2 (635/532)" "FeatureType=Circular" "Barcode=" "BackgroundSubtraction=LocalFeature" "ImageOrigin=1000, 4920" "JpegOrigin=1370, 6000" "Creator=GenePix Pro 6.1.0.4" "Scanner=GenePix 4000B [92479]" "FocusPosition=0" "Temperature=27.18" "LinesAveraged=1" "Comment=" "PMTGain=600 600" "ScanPower=100 100" "LaserPower=3.21 3.68" "Filters=<empty> <empty>" "ScanRegion=100,492,1988,2440" "Supplier=Microarrays, Inc." "Comment=Gal Creator v2.0, 6/25/2007_ann update Dec 2008" "Block" "Column" "Row" "Name" "ID" "X" "Y" "Dia." "F635 Median" "F635 Mean" "F635 SD" "F635 CV" "B635" "B635 Median" "B635 Mean" "B635 SD" "B635 CV" "% > B635+1SD" "% > B635+2SD" "F635 % Sat." "F532 Median" "F532 Mean" "F532 SD" "F532 CV" "B532" "B532 Median" "B532 Mean" "B532 SD" "B532 CV" "% > B532+1SD" "% > B532+2SD" "F532 % Sat." "Ratio of Medians (635/532)" "Ratio of Means (635/532)" "Median of Ratios (635/532)" "Mean of Ratios (635/532)" "Ratios SD (635/532)" "Rgn Ratio (635/532)" "Rgn R2 (635/532)" "F Pixels" "B Pixels" "Circularity" "Sum of Medians (635/532)" "Sum of Means (635/532)" "Log Ratio (635/532)" "F635 Median - B635" "F532 Median - B532" "F635 Mean - B635" "F532 Mean - B532" "F635 Total Intensity" "F532 Total Intensity" "SNR 635" "SNR 532" "Flags" "Normalize" "Autoflag" 1 1 1 "15: D-01" "Dye Marker" 1650 6270 100 41 103 171 166 36 36 37 11 29 36 23 0 4357 18931 24978 131 83 83 93 49 52 97 97 16 0.001 0.004 0.002 0.002 5.029 0.004 0.535 80 560 100 4279 18915 -9.739 5 4274 67 18848 8258 1514490 6.000 384.449 0 0 0

Dear Chris, you have omitted the output of sessionInfo(), so we don't know your OS and package versions and, in particular, the LOCALE the error message complains about, but since it is almost the same message as in this recent thread, Martin's posting may be helpful: http://article.gmane.org/gmane.science.biology.informatics.conductor/2 4988/match=locale Cheers, - axel Axel Klenk Research Informatician Actelion Pharmaceuticals Ltd / Gewerbestrasse 16 / CH-4123 Allschwil / Switzerland Chris Fenton <chrisf at="" fagmed.ui="" t.no=""> To Sent by: bioconductor at stat.math.ethz.ch bioconductor-boun cc ces at stat.math.eth z.ch Subject [BioC] LIMMA problems with gpr file (ATF indentifier ?) 12/17/2009 12:13 PM Been handed a bunch of gpr files this with a two day limit to do the analysis. The problem is that I can not get LIMMA to read the gpr files. Anyone run into this problem ? I have checked the gpr file format and this seems compliant, Yet rg <- read.maimages(files=targets$FileName[1], source='genepix') Error in sub("^\"", "", readLines(con, n = 1)) : input string 1 is invalid in this locale Is this the ATF value ? Chris """ header plus one row """ ATF 1.0 30 56 "Type=GenePix Results 3" "DateTime=2009/12/05 13:29:02" "Settings=" "GalFile=C:\Hilde Sunniva\SunnivaLitRh?st2009\vibrio_v1.0.2.gal" "PixelSize=10" "Wavelengths=635 532" "ImageFiles=C:\Hilde Sunniva\SunnivaLitRhost2009 \2009-12-05_AA_Cy3_hODwt3_Cy5_hODLitR3_12ug_vibrio slide 339709_1 line_Ometning.tif2 C:\Hilde Sunniva\SunnivaLitRhost2009 \2009-12-05_AA_Cy3_hODwt3_Cy5_hODLitR3_12 ug_vibrio slide 339709_1line_Ometning.tif3" "NormalizationMethod=None" "NormalizationFactors=1 1" "JpegImage=C:\HildeSunniva\SunnivaLitRhost2009 \2009-12-05_AA_Cy3_hODwt3_Cy5_hODLitR3_12ug_vibrioslide 339709.jpg" "StdDev=Type 1" "RatioFormulations=W1/W2 (635/532)" "FeatureType=Circular" "Barcode=" "BackgroundSubtraction=LocalFeature" "ImageOrigin=1000, 4920" "JpegOrigin=1370, 6000" "Creator=GenePix Pro 6.1.0.4" "Scanner=GenePix 4000B [92479]" "FocusPosition=0" "Temperature=27.18" "LinesAveraged=1" "Comment=" "PMTGain=600 600" "ScanPower=100 100" "LaserPower=3.21 3.68" "Filters=<empty> <empty>" "ScanRegion=100,492,1988,2440" "Supplier=Microarrays, Inc." "Comment=Gal Creator v2.0, 6/25/2007_ann update Dec 2008" "Block" "Column" "Row" "Name" "ID" "X" "Y" "Dia." "F635 Median" "F635 Mean" "F635 SD" "F635 CV" "B635" "B635 Median" "B635 Mean" "B635 SD" "B635 CV" "% > B635+1SD" "% > B635+2SD" "F635 % Sat." "F532 Median" "F532 Mean" "F532 SD" "F532 CV" "B532" "B532 Median" "B532 Mean" "B532 SD" "B532 CV" "% > B532+1SD" "% > B532+2SD" "F532 % Sat." "Ratio of Medians (635/532)" "Ratio of Means (635/532)" "Median of Ratios (635/532)" "Mean of Ratios (635/532)" "Ratios SD (635/532)" "Rgn Ratio (635/532)" "Rgn R2 (635/532)" "F Pixels" "B Pixels" "Circularity" "Sum of Medians (635/532)" "Sum of Means (635/532)" "Log Ratio (635/532)" "F635 Median - B635" "F532 Median - B532" "F635 Mean - B635" "F532 Mean - B532" "F635 Total Intensity" "F532 Total Intensity" "SNR 635" "SNR 532" "Flags" "Normalize" "Autoflag" 1 1 1 "15: D-01" "Dye Marker" 1650 6270 100 41 103 171 166 36 36 37 11 29 36 23 0 4357 18931 24978 131 83 83 93 49 52 97 97 16 0.001 0.004 0.002 0.002 5.029 0.004 0.535 80 560 100 4279 18915 -9.739 5 4274 67 18848 8258 1514490 6.000 384.449 0 0 0 _______________________________________________ Bioconductor mailing list Bioconductor at stat.math.ethz.ch https://stat.ethz.ch/mailman/listinfo/bioconductor Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor The information of this email and in any file transmitted with it is strictly confidential and may be legally privileged. It is intended solely for the addressee. If you are not the intended recipient, any copying, distribution or any other use of this email is prohibited and may be unlawful. In such case, you should please notify the sender immediately and destroy this email. The content of this email is not legally binding unless confirmed by letter. Any views expressed in this message are those of the individual sender, except where the message states otherwise and the sender is authorised to state them to be the views of the sender's company. For further information about Actelion please see our website at http://www.actelion.com