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

Matthew Ritchie mritchie at wehi.EDU.AU
Thu Aug 13 00:31:04 CEST 2009


Dear Krupa,

I think the problem is that your 'Genepix Results 2' files have been
scanned at slightly different wavelengths to what read.maimages() expects
(633/543 instead of the default 635/532).  Try specifying the 'columns'
argument, e.g.

RG <- read.maimages(Targets,source="genepix",
                    columns=list(R="F633 Mean", G="F543 Mean",
                                 Rb="B633 Median", Gb="B543 Median"))

I hope this helps.  Best wishes,

Matt

> 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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