[BioC] limma and marray data import problem
Piotr Stępniak
piotrek.stepniak at gmail.com
Wed Jun 4 10:06:43 CEST 2008
Dear Gordon,
Thank you very much for your answer. When I try the arguments nrows=2
or 2640 I get the error:
Read 15sz_szk10_Results1.gpr
Error in read.table(file = file, header = TRUE, col.names = allcnames, :
formal argument "nrows" matched by multiple actual arguments
Csv files give the same error with nrows attribute but the do read
fine with the following instruction:
bialkoRaw<- read.maimages( targets$FileName, columns=list(G="Ch1\
Median", Gb="Ch1\ B\ Median", R="Ch2\ Median", Rb="Ch2\ B\ Median"),
sep=",")
And the object is almost fine:
An object of class "RGList"
$G
15sz_szk10_Results1 16kr_szk11_Results1 19sz_szk19_Results1
[1,] 3016 1632 2413
[2,] 2587 1385 2145
[3,] 3088 1526 2015
[4,] 137 109 596
[5,] 137 114 649
20sz_szk9_Results1 22sz_szk18_Results1 26kr_szk12_Results1
[1,] 2529 4421 12481
[2,] 2459 4576 11637
[3,] 2387 4557 10468
[4,] 186 975 2032
[5,] 174 961 906
26sz_szk13_Results1 27sz_szk14_Results1 30kr_szk16_Results1
[1,] 5946 4747 3374
[2,] 5368 4022 2839
[3,] 4368 4251 3526
[4,] 2164 280 210
[5,] 2087 282 221
30sz_szk17_Results1 34kr_szk20_Results1 35kr_szk6_Results1
[1,] 1814 2108 4703
[2,] 2092 1949 4396
[3,] 1830 2094 4634
[4,] 307 910 171
[5,] 255 805 187
35sz_szk7_Results1 38kr_szk6_Results1 ML_szk15_Results1_BRZYDKIE
[1,] 3053 1852 8598
[2,] 2813 1785 7524
[3,] 2755 1683 8625
[4,] 197 631 548
[5,] 227 656 629
ML_szk15_Results1_BRZYDKIEpopluk
[1,] 10964
[2,] 12696
[3,] 13298
[4,] 7176
[5,] 5768
2636 more rows ...
$Gb
15sz_szk10_Results1 16kr_szk11_Results1 19sz_szk19_Results1
[1,] 172 125 1158
[2,] 168 121 1110
[3,] 168 119 1148
[4,] 178 122 1190
[5,] 162 114 1217
20sz_szk9_Results1 22sz_szk18_Results1 26kr_szk12_Results1
[1,] 285 1513 5559
[2,] 345 1533 5839
[3,] 331 1570 5667
[4,] 328 1565 5544
[5,] 299 1644 5369
26sz_szk13_Results1 27sz_szk14_Results1 30kr_szk16_Results1
[1,] 2490 1025 1086
[2,] 2330 962 1078
[3,] 2206 884 1043
[4,] 2307 836 982
[5,] 2349 775 956
30sz_szk17_Results1 34kr_szk20_Results1 35kr_szk6_Results1
[1,] 645 1258 311
[2,] 618 1267 321
[3,] 647 1300 289
[4,] 679 1276 295
[5,] 708 1267 302
35sz_szk7_Results1 38kr_szk6_Results1 ML_szk15_Results1_BRZYDKIE
[1,] 305 294 3992
[2,] 307 274 3759
[3,] 282 273 3575
[4,] 318 292 3419
[5,] 303 302 3123
ML_szk15_Results1_BRZYDKIEpopluk
[1,] 8085
[2,] 7296
[3,] 7552
[4,] 7125
[5,] 6407
2636 more rows ...
$R
15sz_szk10_Results1 16kr_szk11_Results1 19sz_szk19_Results1
[1,] 1487 1054 1149
[2,] 1387 913 1106
[3,] 1559 924 1006
[4,] 147 109 268
[5,] 161 125 273
20sz_szk9_Results1 22sz_szk18_Results1 26kr_szk12_Results1
[1,] 1259 1459 2621
[2,] 1246 1391 2430
[3,] 1231 1483 2373
[4,] 176 197 334
[5,] 173 182 251
26sz_szk13_Results1 27sz_szk14_Results1 30kr_szk16_Results1
[1,] 1604 1183 1181
[2,] 1624 1047 1090
[3,] 1476 1141 1159
[4,] 361 268 139
[5,] 345 276 145
30sz_szk17_Results1 34kr_szk20_Results1 35kr_szk6_Results1
[1,] 1015 1731 1593
[2,] 1198 1776 1618
[3,] 1195 1666 1741
[4,] 269 561 165
[5,] 257 566 161
35sz_szk7_Results1 38kr_szk6_Results1 ML_szk15_Results1_BRZYDKIE
[1,] 1851 1287 2707
[2,] 1819 1224 1981
[3,] 1755 1087 2400
[4,] 208 186 444
[5,] 217 193 487
ML_szk15_Results1_BRZYDKIEpopluk
[1,] 2403
[2,] 2506
[3,] 2733
[4,] 1166
[5,] 1223
2636 more rows ...
$Rb
15sz_szk10_Results1 16kr_szk11_Results1 19sz_szk19_Results1
[1,] 929 176 313
[2,] 943 180 308
[3,] 906 174 306
[4,] 969 171 309
[5,] 991 169 315
20sz_szk9_Results1 22sz_szk18_Results1 26kr_szk12_Results1
[1,] 509 168 816
[2,] 588 173 815
[3,] 592 171 776
[4,] 621 159 785
[5,] 637 162 834
26sz_szk13_Results1 27sz_szk14_Results1 30kr_szk16_Results1
[1,] 683 304 204
[2,] 651 289 196
[3,] 646 279 187
[4,] 665 278 179
[5,] 643 280 179
30sz_szk17_Results1 34kr_szk20_Results1 35kr_szk6_Results1
[1,] 419 667 663
[2,] 410 688 635
[3,] 409 706 648
[4,] 425 703 630
[5,] 419 692 605
35sz_szk7_Results1 38kr_szk6_Results1 ML_szk15_Results1_BRZYDKIE
[1,] 691 525 1518
[2,] 700 520 1330
[3,] 710 506 1216
[4,] 724 474 1111
[5,] 698 454 1075
ML_szk15_Results1_BRZYDKIEpopluk
[1,] 2131
[2,] 2023
[3,] 1857
[4,] 1711
[5,] 1542
2636 more rows ...
$targets
[1] "15sz_szk10_Results1.csv" "16kr_szk11_Results1.csv"
[3] "19sz_szk19_Results1.csv" "20sz_szk9_Results1.csv"
[5] "22sz_szk18_Results1.csv"
11 more rows ...
$source
[1] "generic"
The columns are not shifted to right, so I get the correct Median
values as desired.
However there is something wrong with the object because any following
instructions give this error:
Error in if (is.int(totalPlate)) { : argument is of length zero
Preasumably it is because the printer layout is missing, so I do this:
bialkoRaw$printer<-getLayout("bialko.gal")
Error in getLayout("bialko.gal") :
gal needs to have columns Block, Row and Column
Strange enough the function readGAL works, but if I try to replace the
above instruction there is no printer parameters like ngrid.c, ngrid.r
etc. just and array.
Is there a way to check RGList object integrity?
Kind Regards,
Piotrek
On Wed, Jun 4, 2008 at 6:56 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
> Dear Piotr,
>
> I can't diagnose your problem, because the shortened version of your data
> file that you emailed reads fine for me when I put the lines in a text file,
> as I show below. I used sep="" in my code because email doesn't preserve
> tab separators. Presumably the problem appears further into the file,
> perhaps near the bottom. Or else you file has inconsistent separators.
>
> Can you try the arguments nrows=2 and nrows=2640?
>
> I would also expect the csv file to read with the following:
>
> read.maimages("file.csv",columns=list(G="F543 Median",Gb="B543 Median",
> R="F633 Median", Rb="B633 Median"),sep=",",nrows=2640)
>
> Best wishes
> Gordon
>
> My code:
>
>> read.maimages("temp.txt",source="genepix",columns=list(G="F543 Median",
>
> Gb="B543 Median", R="F633 Median", Rb="B633 Median"),sep="")
> Read temp.txt
> An object of class "RGList"
> $G
> temp
> [1,] 5946
> [2,] 5368
>
> $Gb
> temp
> [1,] 2490
> [2,] 2330
>
> $R
> temp
> [1,] 1604
> [2,] 1624
>
> $Rb
> temp
> [1,] 683
> [2,] 651
>
> $targets
> FileName
> temp temp.txt
>
> $genes
> Block Row Column ID Name
> 1 1 1 1 2078 ERG_Operon
> 2 1 1 2 2078 ERG_Operon
>
> $source
> [1] "genepix"
>
> $printer
> $ngrid.r
> [1] 1
>
> $ngrid.c
> [1] 1
>
> $nspot.r
> [1] 1
>
> $nspot.c
> [1] 2
>
> attr(,"class")
> [1] "PrintLayout"
>
>
> On Mon, 2 Jun 2008, Piotr Stêpniak wrote:
>
>> Dear Gordon,
>>
>> Thank you for your reply.
>>
>> I tried using source="genepix", it did not work better than "scanarray".
>> The following commands give:
>>
>>> bialkoRaw<-read.maimages(dir(pattern="gpr"), source="genepix")Error in
>>> read.table(file = file, header = TRUE, col.names = allcnames, :
>>
>> duplicate 'row.names' are not allowed
>>
>> It turnes out the format is not 100% valid GenePix, e.g. it does not
>> have any index column, so I try this:
>>
>>> bialkoRaw<-read.maimages(dir(pattern="gpr"), source="genepix",
>>> row.names=NULL)
>>
>> Error in RG[[a]][, i] <- obj[, columns[[a]]] :
>> number of items to replace is not a multiple of replacement length
>> In addition: Warning message:
>> In getLayout(RG$genes, guessdups = FALSE) : NAs introduced by coercion
>>
>> I tried different parameter combinations which got me to the command
>> you've seen in the previous messages (I'm sorry for sending it 3
>> times...).
>>
>> The file is finally read, but wrongly as described earlier.
>>
>> Same happens to gal file:
>>
>>> gal<-readGAL("Bialko.gal")
>>
>> Error in read.table(file = file, header = TRUE, col.names = allcnames, :
>> duplicate 'row.names' are not allowed
>>
>>> gal<-readGAL("Bialko.gal", row.names=NULL)
>>
>> Error in if (is.int(totalPlate)) { : argument is of length zero
>>
>> To answer your further questions shortly:
>> 2. Yes, these are the files straight from the scanner software.
>> ScanArrayExpress also offers csv export, but reading them is another
>> problem. They do have Index column,
>>>
>>> bialkoRaw<- read.maimages( dir(pattern="csv"), columns=list(G="Ch1\
>>> Median", Gb="Ch1\ B\ Median", R="Ch2\ Median", Rb="Ch2\ B\ Median"),
>>> sep=",")
>>
>> reads the file and the values are under correct columns but I get no
>> printer layout read and other function to process the data gives:
>> Error in if (is.int(totalPlate)) { : argument is of length zero
>>
>> 3. Yes, I'd be happy to if you please look at it:
>>
>> Beginning of GPR file:
>>
>> ATF 1.0
>>
>> 21 82
>>
>> "Type=GenePix Results 2"
>>
>> "DateTime=2008/03/28 10:30:03"
>>
>> "Settings=Easy Quant"
>>
>> "GalFile=D:\Luiza\Grant bialaczkowy_BADANIA\BIALACZKI_skany\DRUGI
>> RZUT\BIALACZKI_2_25luty2008_popr.gal"
>>
>> "Scanner=Model: Express Serial No.: 432617"
>>
>> "Comment=<F1>Alexa 555<F2>Alexa 647<F1 Offset>0,0<F2 Offset>0,0<Comment>"
>>
>> "PixelSize=10"
>>
>> "Wavelengths=543 nm 633 nm"
>>
>> "ImageFiles=D:\Luiza\Grant bialaczkowy_BADANIA\BIALACZKI_skany\DRUGI
>> RZUT\12_03_2008\Skan
>> Agi\HL60_szk13_PMT65_roz10_Alexa555.tif D:\Luiza\Grant
>> bialaczkowy_BADANIA\BIALACZKI_skany\DRUGI RZUT\12_03_2008\Skan
>> Agi\26sz_szk13_PMT60_roz10_Alexa647.tif"
>>
>> "PMTGain=65 60"
>>
>> "NormalizationMethod=LOWESS"
>>
>> "NormalizationFactors=0.000 0.000"
>>
>> "JpegImage="
>>
>> "RatioFormulations=W2/W1(633/543)"
>>
>> "Barcode="
>>
>> "ImageOrigin=1500 11600"
>>
>> "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 R² (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 R²
>> (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 R²
>> (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 ERG_Operon 2078 2805 13125 230
>> 5946 6035 1754 2490 2506 529 97 92 0 1604
>> 1636 517 683 698 194 94 84 0 0 0
>> 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 0.266 0.269
>> 0.270 0.329 0.329 0.232 0.621 0.000 0.000 0.000 0.000
>> 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>> 0.000 384 734 4377 4498 -1.908 0.000 0.000 3456 921
>> 0 0 3545 953 0 0 100 1
>>
>> 1 2 1 ERG_Operon 2078 3250 13128 220
>> 5368 5457 1634 2330 2378 537 96 91 0 1624
>> 1651 531 651 671 188 95 88 0 0 0
>> 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 0.320 0.320
>> 0.318 0.567 0.567 0.254 0.608 0.000 0.000 0.000 0.000
>> 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>> 0.000 351 858 4011 4127 -1.643 0.000 0.000 3038 973
>> 0 0 3127 1000 0 0 100 1
>>
>> 1 3 1 ERG_Operon 2078 3698 13124 220
>> 4368 4676 1646 2206 2240 490 90 81 0 1476
>> 1562 592 646 673 182 90 80 0 0 0
>> 0 0 0 0 0 0 0 0 0
>> 0 0 0 0 0 0 0 0.384 0.371
>> 0.377 0.498 0.498 0.281 0.610 0.000 0.000 0.000 0.000
>> 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000 0.000
>> 0.000 348 858 2992 3386 -1.381 0.000 0.000 2162 830
>> 0 0 2470 916 0 0 100 1
>>
>> And for comparison here is a corresponding csv:
>>
>> BEGIN HEADER
>>
>> PerkinElmer Inc.
>>
>> ScanArrayCSVFileFormat,2.00
>>
>> ScanArray Express,2.00
>>
>> Number_of_Columns,62
>>
>> END HEADER
>>
>>
>>
>> BEGIN GENERAL INFO
>>
>> DateTime,2008/03/28 10:30
>>
>> GalFile,D:\Luiza\Grant bialaczkowy_BADANIA\BIALACZKI_skany\DRUGI
>> RZUT\BIALACZKI_2_25luty2008_popr.gal
>>
>> Scanner,Model: Express Serial No.: 432617
>>
>> User Name,Luiza
>>
>> Computer Name,
>>
>> Protocol,Easy Quant
>>
>> Quantitation Method,Adaptive Circle
>>
>> Quality Confidence Calculation,Footprint
>>
>> User comments,
>>
>> Image Origin,1500,11600
>>
>> Temperature,0
>>
>> Laser Powers,90,90
>>
>> Laser On Time,0
>>
>> PMT Voltages,65,60
>>
>> END GENERAL INFO
>>
>>
>>
>> BEGIN QUANTITATION PARAMETERS
>>
>> Min Percentile,30
>>
>> Max Percentile,300
>>
>> END QUANTITATION PARAMETERS
>>
>>
>>
>> BEGIN QUALITY MEASUREMENTS
>>
>> Max Footprint,100
>>
>> END QUALITY MEASUREMENTS
>>
>>
>>
>> BEGIN ARRAY PATTERN INFO
>>
>> Units,µm
>>
>> Array Rows,10
>>
>> Array Columns,4
>>
>> Spot Rows,9
>>
>> Spot Columns,9
>>
>> Array Row Spacing,4500.000000
>>
>> Array Column Spacing,4500.000000
>>
>> Spot Row Spacing,450.000000
>>
>> Spot Column Spacing,450.000000
>>
>> Spot Diameter,200
>>
>> Interstitial,0
>>
>> Spots Per Array,81
>>
>> Total Spots,2640
>>
>> END ARRAY PATTERN INFO
>>
>>
>>
>> BEGIN IMAGE INFO
>>
>> ImageID,Channel,Image,Fluorophore,Barcode,Units,X Units Per Pixel,Y
>> Units Per Pixel,X Offset,Y Offset,Status
>>
>> -1,CH1,D:\Luiza\Grant bialaczkowy_BADANIA\BIALACZKI_skany\DRUGI
>> RZUT\12_03_2008\Skan Agi\HL60_szk13_PMT65_roz10_Alexa555.tif,Alexa
>> 555,,µm,10.000000,10.000000,0.000000,0.000000,Control Image
>>
>> -1,CH2,D:\Luiza\Grant bialaczkowy_BADANIA\BIALACZKI_skany\DRUGI
>> RZUT\12_03_2008\Skan Agi\26sz_szk13_PMT60_roz10_Alexa647.tif,Alexa
>> 647,,µm,10.000000,10.000000,0.000000,0.000000,
>>
>> END IMAGE INFO
>>
>>
>>
>> BEGIN NORMALIZATION INFO
>>
>> Normalization Method,LOWESS
>>
>> END NORMALIZATION INFO
>>
>>
>>
>> BEGIN DATA
>>
>> Index,Array Row,Array Column,Spot Row,Spot
>> Column,Name,ID,X,Y,Diameter,F Pixels,B Pixels,Footprint,Flags,Ch1
>> Median,Ch1 Mean,Ch1 SD,Ch1 B Median,Ch1 B Mean,Ch1 B SD,Ch1 % > B + 1
>> SD,Ch1 % > B + 2 SD,Ch1 F % Sat.,Ch1 Median - B,Ch1 Mean - B,Ch1
>> SignalNoiseRatio,Ch2 Median,Ch2 Mean,Ch2 SD,Ch2 B Median,Ch2 B
>> Mean,Ch2 B SD,Ch2 % > B + 1 SD,Ch2 % > B + 2 SD,Ch2 F % Sat.,Ch2
>> Median - B,Ch2 Mean - B,Ch2 SignalNoiseRatio,Ch2 Ratio of Medians,Ch2
>> Ratio of Means,Ch2 Median of Ratios,Ch2 Mean of Ratios,Ch2 Ratios
>> SD,Ch2 Rgn Ratio,Ch2 Rgn R²,Ch2 Log Ratio,Sum of Medians,Sum of
>> Means,Ch1 N Median,Ch1 N Mean,Ch1 N (Median-B),Ch1 N (Mean-B),Ch2 N
>> Median,Ch2 N Mean,Ch2 N (Median-B),Ch2 N (Mean-B),Ch2 N Ratio of
>> Medians,Ch2 N Ratio of Means,Ch2 N Median of Ratios,Ch2 N Mean of
>> Ratios,Ch2 N Rgn Ratio,Ch2 N Log Ratio
>>
>>
>> 1,1,1,1,1,"ERG_Operon","2078",2805,13125,230,384,734,0,3,5946,6035,1754.26,2490,2506,529.19,97.4,92.2,0.0,3456,3545,11.24,1604,1636,517.27,683,698,194.19,94.3,84.1,0.0,921,953,8.26,0.27,0.27,0.27,0.33,0.39,0.23,0.62,-1.908,4377,4498,5946,6035,3456,3545,3027,2984,1446,2664,0.42,0.75,0.42,0.92,0.44,-1.257
>>
>>
>> 2,1,1,1,2,"ERG_Operon","2078",3250,13128,220,351,858,0,3,5368,5457,1634.22,2330,2378,537.27,96.0,90.9,0.0,3038,3127,9.99,1624,1651,531.34,651,671,188.42,94.9,88.0,0.0,973,1000,8.62,0.32,0.32,0.32,0.57,2.14,0.25,0.61,-1.643,4011,4127,5368,5457,3038,3127,3100,3039,1536,2956,0.51,0.95,0.50,1.68,0.48,-0.984
>>
>>
>> 3,1,1,1,3,"ERG_Operon","2078",3698,13124,220,348,858,0,3,4368,4676,1645.59,2206,2240,490.01,90.2,81.0,0.0,2162,2470,8.91,1476,1562,591.68,646,673,182.34,90.2,80.2,0.0,830,916,8.09,0.38,0.37,0.38,0.50,0.92,0.28,0.61,-1.381,2992,3386,4368,4676,2162,2470,2947,2941,283,797,0.13,0.32,0.13,0.43,0.56,-2.934
>>
>>
>> Kind Regards,
>> Piotr
>>
>> On Mon, Jun 2, 2008 at 3:57 AM, Gordon K Smyth <smyth at wehi.edu.au> wrote:
>>>
>>> Dear Piotr,
>>>
>>> The file extension "gpr" is short for GenePix Results file. If ScanArray
>>> Express outputs a file with this extension, you should have every
>>> expectation that is formated exactly the same as a gpr file from GenePix,
>>> and therefore you should be able to read it using
>>> read.maimages(source="genepix"). If this is not true, then ScanArray is
>>> irresponsible to use this extension.
>>>
>>> Same comments for the GAL file. It is obviously not a GAL file as
>>> defined
>>> by GenePix, otherwise it would be read using readGAL().
>>>
>>> From your description below, a possible explanation for the problem is
>>> that
>>> your files have an extra column with no corresponding heading, e.g., a
>>> column of row numbers. However no one on this mailing list can tell that
>>> for sure without you showing us some lines from your file.
>>>
>>> Questions:
>>> 1. Why have you set row.names=NULL? This prevents R from detecting a
>>> column
>>> of row numbers. What happens if you remove this?
>>>
>>> 2. Are these files exactly as output by ScanArray, or have they been
>>> further
>>> processed?
>>>
>>> 3. Can you post the first few lines of an example file?
>>>
>>> Best wishes
>>> Gordon
>>>
>>> PS. You posted the same question to the BioC mailing list on three
>>> consecutive days during the weekend. Please post the question just once.
>>>
>>>
>>>> Date: Sat, 31 May 2008 12:55:25 +0200
>>>> From: " Piotr St?pniak " <piotrek.stepniak at gmail.com>
>>>> Subject: [BioC] limma and marray data import problem
>>>> To: bioconductor at stat.math.ethz.ch
>>>>
>>>> Hello Everyone,
>>>>
>>>> I am Piotr St?pniak, B.Sc. in Biotechnology, currently under M.Sc.
>>>> course at Adam Mickiewicz University in Pozna?, Poland. I am working
>>>> in Polish Science Academy in microarray experiments group.
>>>>
>>>> I'm a newbie in R and BioC, so please forgive me if my question is
>>>> easy...
>>>>
>>>> I'm having problem with data import to RGList or marrayRaw objects.
>>>> Using the following instruction:
>>>> bialkoRaw<- read.maimages( dir(pattern="gpr"), columns=list(G="F543
>>>> Median", Gb="B543 Median", R="F633 Median", Rb="B633 Median"),
>>>> annotation=c("Block", "Column", "Row", "Name", "ID"), row.names=NULL)
>>>> The data seems to load, but $genes table looks odd, I guess the column
>>>> names are shifted right by 1 column:
>>>> $genes
>>>> Block Column Row Name ID
>>>> 1 1 1 ERG_Operon 2078 2647
>>>> 2 2 1 ERG_Operon 2078 3102
>>>> 3 3 1 ERG_Operon 2078 3549
>>>> 4 4 1 FLT3_Operon 2322 3994
>>>> 5 5 1 FLT3_Operon 2322 4444
>>>> 2635 more rows ...
>>>> This I think causes printer layout to be imported wrongly and then any
>>>> other try to process the data (e.g. quality tests) produce such error
>>>> message:
>>>> Error in if (is.int(totalPlate)) { : argument is of length zero
>>>>
>>>> The data is obtained with ScanArrayExpress software, so I have it in
>>>> gpr or csv files, both give similar errors, but loading csv files
>>>> seems also to fail import values for each channel and gets only the
>>>> file name headers.
>>>>
>>>> Marray import also fails, I will skip the info about it not to enlarge
>>>> the mail unnecessarily.
>>>>
>>>> My R session info is as follows:
>>>>>
>>>>> sessionInfo()
>>>>
>>>> R version 2.6.2 (2008-02-08)
>>>> i486-pc-linux-gnu
>>>>
>>>> locale:
>>>> C
>>>>
>>>> attached base packages:
>>>> [1] grid splines tools stats graphics grDevices utils
>>>> [8] datasets methods base
>>>>
>>>> other attached packages:
>>>> [1] arrayQuality_1.18.0 gridBase_0.4-3 hexbin_1.14.0
>>>> [4] convert_1.16.0 RColorBrewer_1.0-2 cluster_1.11.10
>>>> [7] arrayMagic_1.16.1 genefilter_1.16.0 survival_2.34-1
>>>> [10] marray_1.18.0 vsn_3.6.0 limma_2.14.1
>>>> [13] affy_1.16.0 preprocessCore_1.0.0 affyio_1.8.0
>>>> [16] Biobase_1.16.3 lattice_0.17-7
>>>>
>>>> loaded via a namespace (and not attached):
>>>> [1] AnnotationDbi_1.0.6 DBI_0.2-4 RSQLite_0.6-8
>>>> [4] annotate_1.18.0 rcompgen_0.1-17
>>>>
>>>>
>>>> I think I should also say that these data causes import problems to
>>>> any other data analysis software :( I also tried to read the printer
>>>> layout from gal file, but all I got was "Block, Row, Column, ID
>>>> columns not found" error.
>>>>
>>>> I'd greatly appreciate any help, please.
>>>>
>>>> Yours faithfully,
>>>> Piotr St?pniak
>>>
>
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