[BioC] LIMMA problems with gpr file (ATF indentifier ?)
Chris Fenton
chrisf at fagmed.uit.no
Thu Dec 17 12:13:56 CET 2009
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\SunnivaLitRhøst2009\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
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