LIMMA problems with gpr file (ATF indentifier ?)
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@gordon-smyth
Last seen 4 minutes ago
WEHI, Melbourne, Australia
Dear Chris, No, it doesn't appear to be the ATF value. The function which is failing is readGPRHeader(). The error message suggests that this is failing because of a double-quote character as the first character on a line. This shouldn't normally cause any problems, so the error is probably to do with non-English (Norwegian?) character settings either in the GPR file or in your version of R. This is an R issue rather than a limma issue. Best wishes Gordon > Date: Thu, 17 Dec 2009 12:13:56 +0100 > From: Chris Fenton <chrisf at="" fagmed.uit.no=""> > Subject: [BioC] LIMMA problems with gpr file (ATF indentifier ?) > To: bioconductor at stat.math.ethz.ch > Message-ID: <1261048436.22359.14.camel at microarray> > Content-Type: text/plain; charset=UTF-8 > > 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 ______________________________________________________________________ The information in this email is confidential and intend...{{dropped:4}}
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