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

Thu Dec 17 13:31:02 CET 2009

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/24988/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\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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