[BioC] LIMMA problems with gpr file (ATF indentifier ?)
Gordon K Smyth
smyth at wehi.EDU.AU
Sat Dec 19 03:28:25 CET 2009
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
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