[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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