[BioC] LIMMA problems with gpr file (ATF indentifier ?)

[Chris Fenton]

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