[BioC] Read.maimages Error reading 'Genepix results file 2' version files

Wed Aug 12 17:50:57 CEST 2009

Hi

I have a problem in reading the Genepix files using 'read.maimages' function
of limma package. My GPR files are in 'Genepix Results 2' format. However
another set of example GPR files in 'Genepix Results 3' format can be read.
Please find the details below. I will appreciate feedback. Thanks -Krupa

--------------------------
R-version:
> sessionInfo()
R version 2.9.1 (2009-06-26)
i386-apple-darwin8.11.1

locale:
en_GB.UTF-8/en_GB.UTF-8/C/C/en_GB.UTF-8/en_GB.UTF-8

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
[1] limma_2.18.2
-----------------------------
Function: readTargets works fine.
> Targets <- readTargets("Targets_10_30.txt")
> show (Targets)
  Slide.Number     FileName Cy3 Cy5
1          149 slide149.gpr 10A 30A
2          150 slide159.gpr 30A 10A
3          152 slide152.gpr 10B 30B
4          153 slide153.gpr 30B 10B
5          154 slide154.gpr 10C 30C
6          155 slide155.gpr 30C 10C
7          156 Slide156.gpr 10D 30D
8          157 Slide157.gpr 30D 10D
--------------------------------------
Function: read.maimages does not work
> RG <- read.maimages(Targets,source="genepix")
Error in read.table(file = file, header = TRUE, col.names = allcnames,  :
  duplicate 'row.names' are not allowed
-----------------------------------------

Example GPR file header

 ATF 1
 21 82
 Type=GenePix Results 2
 DateTime=2009/08/07 09:05:51
 Settings=C. elegans oligo
 GalFile=C:\scananal\Gal files for ScanArray\Celegans_oligo_GAL.gal
 Scanner=Model: ScanArray Express HT Serial No.: 680078
 Comment=<F1>Cyanine 3<F2>Cyanine 5<F1 Offset>0,0<F2 Offset>1,0<Comment>
 PixelSize=10
 Wavelengths=543 nm 633 nm
 ImageFiles=C:\scananal\Images\C. elegans oligo batch 26\Slide
149_Cyanine3_Celegans_oligo_1347.tif C:\scananal\Images\C. elegans oligo
batch 26\Slide 149_Cyanine5_Celegans_oligo_1347.tif
 PMTGain=80 62
 NormalizationMethod=LOWESS
 NormalizationFactors=0.000 0.000
 JpegImage=
 RatioFormulations=W2/W1(633/543)
 Barcode=
 ImageOrigin=0 4481
 JpegOrigin=0 0
 Creator=ScanArray Express, Microarray Analysis System 3.0.0.16
 Temperature=0.0
 LaserPower=90 90 0 0
 LaserOnTime=0 0 0 0
 Block Column Row Name ID X Y Dia. F543 Median F543 Mean F543 SD B543 Median
B543 Mean B543 SD % > B543+1SD % > B543+2SD F543 % Sat. F633 Median F633
Mean F633 SD B633 Median B633 Mean B633 SD % > B633+1SD % > B633+2SD F633 %
Sat. F3 Median F3 Mean F3 SD B3 Median B3 Mean B3 SD % > B3+1SD % > B3+2SD
F3 % Sat. F4 Median F4 Mean F4 SD B4 Median B4 Mean B4 SD % > B4+1SD % >
B4+2SD F4 % Sat. Ratio of Medians (633/543) Ratio of Means (633/543) Median
of Ratios (633/543) Mean of Ratios (633/543) Ratios SD (633/543) Rgn Ratio
(633/543) Rgn R¾ (633/543) Ratio of Medians (Ratio/2) Ratio of Means
(Ratio/2) Median of Ratios (Ratio/2) Mean of Ratios (Ratio/2) Ratios SD
(Ratio/2) Rgn Ratio (Ratio/2) Rgn R¾ (Ratio/2) Ratio of Medians (Ratio/3)
Ratio of Means (Ratio/3) Median of Ratios (Ratio/3) Mean of Ratios (Ratio/3)
Ratios SD (Ratio/3) Rgn Ratio (Ratio/3) Rgn R¾ (Ratio/3) F Pixels B Pixels
Sum of Medians Sum of Means Log Ratio (633/543) Log Ratio (Ratio/2) Log
Ratio (Ratio/3) F543 Median - B543 F633 Median - B633 F3 Median - B3 F4
Median - B4 F543 Mean - B543 F633 Mean - B633 F3 Mean - B3 F4 Mean - B4
Flags Normalize
 1 1 1 Spot Report 1 - Cab Spot Report 1 - Cab 2467 6862 80 301 501 487 203
354 350 28 13 0 2095 2131 561 229 243 98 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 19.041 6.383 7.399 27.002 27.002 0.869 0.569 0 0 0 0 0 0 0 0 0 0 0
0 0 0 39 236 1964 2200 4.251 0 0 98 1866 0 0 298 1902 0 0 100 1
 1 2 1 C25A1.8 cea2.c.00914 2678 6848 100 10420 10445 2870 197 347 317 100
100 0 9139 9172 2403 245 288 145 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0.87 0.871 0.87 0.903 0.903 0.638 0.58 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 180
19117 19175 -0.201 0 0 10223 8894 0 0 10248 8927 0 0 100 1
 1 3 1 F21F3.6 cea2.c.02677 2877 6855 100 13934 14087 4202 258 393 368 100
100 0 20164 20572 5319 275 323 171 100 100 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
0 0 1.454 1.468 1.46 1.663 1.663 1.023 0.653 0 0 0 0 0 0 0 0 0 0 0 0 0 0 62
180 33565 34126 0.54 0 0 13676 19889 0 0 13829 20297 0 0 100 1
---------------------------------------------------------------------------

However another set of gpr files (from Limma examples) can be read using
'read.maimages' function. Header of the example file that works.

 ATF 1
 29 52
 Type=GenePix Results 3
 DateTime=2003/08/07 10:08:35
 Settings=E:\Madeleine's Data\Microarray\Human\GPR\6Hs.166.gps
 GalFile=E:\Madeleine's Data\Microarray\Gal File\6Hs.gal
 PixelSize=10
 Wavelengths=635 532
 ImageFiles=E:\Madeleine's Data\Microarray\Human\SCANS\6Hs.166.tif 2
E:\Madeleine's Data\Microarray\Human\SCANS\6Hs.166.tif 3
 NormalizationMethod=None
 NormalizationFactors=1 1
 JpegImage=E:\Madeleine's Data\Microarray\Human\GPR\6Hs.166.jpg
 StdDev=Type 1
 RatioFormulations=W1/W2 (635/532)
 FeatureType=Circular
 Barcode=
 BackgroundSubtraction=LocalFeature
 ImageOrigin=1360, 14520
 JpegOrigin=0, 0
 Creator=GenePix Pro 5.0.1.2
 Scanner=GenePix 4000B [83306]
 FocusPosition=0
 Temperature=21.44
 LinesAveraged=2
 Comment=
 PMTGain=760 570
 ScanPower=100 100
 LaserPower=3.25 3.54
 Filters=
 ScanRegion=136,1452,1924,6860
 Supplier=
 Block Column Row Name ID X Y Dia. F635 Median F635 Mean F635 SD B635 B635
Median B635 Mean B635 SD % > B635+1SD % > B635+2SD F635 % Sat. F532 Median
F532 Mean F532 SD B532 B532 Median B532 Mean B532 SD % > 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 R¾ (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 OVGP1 - Oviductal glycoprotein 1, 120kD (mucin 9, oviductin)
H200000297 1700 14710 120 139 154 70 137 137 148 66 18 6 0 189 201 66 191
191 194 46 18 11 0 -1 1.7 0.975 1.17 3.532 2.323 0.061 120 734 100 0 27
Error 2 -2 17 10 18463 24089 0.091 0.152 -50 0 0
 1 2 1 TAF1 - TAF1 RNA polymerase II, TATA box binding protein
(TBP)-associated factor, 250 kD H200000303 1880 14710 70 181 207 109 142 142
149 57 37 21 0 255 260 60 194 194 196 42 65 34 0 0.639 0.985 0.886 0.86
3.551 4.153 0.031 32 236 100 100 131 -0.645 39 61 65 66 6623 8328 1.018
1.524 0 0 0

Thank you.

Krupa

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