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Sample GSM184226 Query DataSets for GSM184226
Status Public on Aug 09, 2007
Title mk291c1-2 grn bkgd
Sample type genomic
 
Channel 1
Source name 0.25 ng 26695/J99 genomic DNA mix
Organism Helicobacter pylori
Characteristics 0.25 ng 26695/J99 genomic DNA mix
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 500 ng mk291c1-2 grn bkgd
Organism Helicobacter pylori
Characteristics 500 ng mk291c1-2 grn bkgd
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy5
Label protocol not provided
 
 
Hybridization protocol not provided
Scan protocol not provided
Feature Extraction; Software and parameters for feature extraction.; Protocol Type = Feature Extraction; Parameter Image Origin = 2320, 9560; Parameter Datafile type = GenePix Results 3; Software: type: feature extraction; Performer: Nina,,Salama
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.37; Parameter Scan Time = 17:29:32; Parameter PMT Volts = 750; Parameter Scan Date = 2004-11-27; Parameter Pixel Size = 10; Parameter Laser on time = 54232; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 5.44; Parameter Scan Power = 10; Parameter Scanning software version = 2.0.3.1; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 32.37; Parameter Scan Time = 17:29:32; Parameter PMT Volts = 620; Parameter Scan Date = 2004-11-27; Parameter Pixel Size = 10; Parameter Laser on time = 54008; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.81; Parameter Scanning software version = 2.0.3.1; Parameter Scan Power = 33; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2004-11/57720.gif
Data processing VALUE is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Apr 25, 2007
Last update date Aug 08, 2007
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2781
Series (1)
GSE7618 Array CGH of Mexican Patient Isolates and BCS100 Strain

Data table header descriptions
ID_REF ID_REF
CH1I_MEAN Mean feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEAN Mean feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEDIAN The median feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_MEDIAN The median feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH1D_MEAN The mean feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2D_MEAN .The mean feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1I_MEDIAN Median feature pixel intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale
CH2I_MEDIAN Median feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale
CH1B_MEAN The mean feature background intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Background
CH2B_MEAN The mean feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Background
CH1D_MEDIAN The median feature pixel intensity at wavelength 532 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH2D_MEDIAN The median feature pixel intensity at wavelength 635 nm with the median background subtracted.; Type: integer; Scale: linear_scale
CH1_PER_SAT The percentage of feature pixels at wavelength 532 nm that are saturated.; Type: integer; Scale: linear_scale
CH2_PER_SAT The percentage of feature pixels at wavelength 635 nm that are saturated.; Type: integer; Scale: linear_scale
CH1I_SD The standard deviation of the feature intensity at wavelength 532 nm.; Type: integer; Scale: linear_scale; Channel: Cy3 Channel
CH2I_SD The standard deviation of the feature pixel intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH1B_SD The standard deviation of the feature background intensity at wavelength 532 nm.; Type: float; Scale: linear_scale; Channel: Cy3 Channel; Background
CH2B_SD The standard deviation of the feature background intensity at wavelength 635 nm.; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
PERGTBCH1I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_1SD The percentage of feature pixels with intensities more than one standard deviation above the background pixel intensity, at wavelength 635 nm.; Type: integer; Scale: linear_scale
PERGTBCH1I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
PERGTBCH2I_2SD The percentage of feature pixels with intensities more than two standard deviations above the background pixel intensity, at wavelength 532 nm.; Type: integer; Scale: linear_scale
SUM_MEAN The sum of the arithmetic mean intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
SUM_MEDIAN The sum of the median intensities for each wavelength, with the median background subtracted.; Type: integer; Scale: linear_scale
RAT1_MEAN Ratio of the arithmetic mean intensities of each spot for each wavelength, with the median background subtracted. Channel 1/Channel 2 ratio, (CH1I_MEAN - CH1B_MEDIAN)/(CH2I_MEAN - CH2B_MEDIAN) or Green/Red ratio.; Type: float; Scale: linear_scale
RAT2_MEAN The ratio of the arithmetic mean intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_MEDIAN The ratio of the median intensities of each feature for each wavelength, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEAN The geometric mean of the pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
PIX_RAT2_MEDIAN The median of pixel-by-pixel ratios of pixel intensities, with the median background subtracted.; Type: float; Scale: linear_scale
RAT2_SD The geometric standard deviation of the pixel intensity ratios.; Type: float; Scale: linear_scale
TOT_SPIX The total number of feature pixels.; Type: integer; Scale: linear_scale
TOT_BPIX The total number of background pixels.; Type: integer; Scale: linear_scale
REGR The regression ratio of every pixel in a 2-feature-diameter circle around the center of the feature.; Type: float; Scale: linear_scale
CORR The correlation between channel1 (Cy3) & Channel 2 (Cy5) pixels within the spot, and is a useful quality control parameter. Generally, high values imply better fit & good spot quality.; Type: float; Scale: linear_scale
DIAMETER The diameter in um of the feature-indicator.; Type: integer; Scale: linear_scale
X_COORD X-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
Y_COORD Y-coordinate of the center of the spot-indicator associated with the spot, where (0,0) is the top left of the image.; Type: integer; Scale: linear_scale
TOP Box top: int(((centerX - radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
BOT Box bottom: int(((centerX + radius) - Xoffset) / pixelSize).; Type: integer; Scale: linear_scale
LEFT Box left: int(((centerY - radius) - yoffset) / pixelSize).; Type: integer; Scale: linear_scale
RIGHT Box right: int(((centerY + radius) - yoffset) / pixelSize); Type: integer; Scale: linear_scale
FLAG The type of flag associated with a feature: -100 = user-flagged null spot; -50 = software-flagged null spot; 0 = spot valid.; Type: integer; Scale: linear_scale
CH2IN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized value of mean Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
RAT2N_MEAN Type: float; Scale: linear_scale
CH2IN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized value of median Channel 2 (usually 635 nm) intensity with normalized background subtracted (CH2IN_MEDIAN - CH2BN_MEDIAN).; Type: integer; Scale: linear_scale
RAT1N_MEAN Ratio of the means of Channel 1 (usually 532 nm) intensity to normalized Channel 2 (usually 635 nm) intensity with median background subtracted (CH1D_MEAN/CH2DN_MEAN). Channel 1/Channel 2 ratio normalized or Green/Red ratio normalized.; Type: float; Scale: linear_scale
RAT2N_MEDIAN Channel 2/Channel 1 ratio normalized, RAT2_MEDIAN/Normalization factor or Red/Green median ratio normalized.; Type: float; Scale: linear_scale
LOG_RAT2N_MEAN Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEAN)].; Type: float; Scale: log_base_2
VALUE Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm) [log (base 2) (RAT2N_MEDIAN)].; Type: float; Scale: log_base_2

Data table
ID_REF CH1I_MEAN CH2I_MEAN CH1B_MEDIAN CH2B_MEDIAN CH1D_MEAN CH2D_MEAN CH1I_MEDIAN CH2I_MEDIAN CH1B_MEAN CH2B_MEAN CH1D_MEDIAN CH2D_MEDIAN CH1_PER_SAT CH2_PER_SAT CH1I_SD CH2I_SD CH1B_SD CH2B_SD PERGTBCH1I_1SD PERGTBCH2I_1SD PERGTBCH1I_2SD PERGTBCH2I_2SD SUM_MEAN SUM_MEDIAN RAT1_MEAN RAT2_MEAN RAT2_MEDIAN PIX_RAT2_MEAN PIX_RAT2_MEDIAN RAT2_SD TOT_SPIX TOT_BPIX REGR CORR DIAMETER X_COORD Y_COORD TOP BOT LEFT RIGHT FLAG CH2IN_MEAN CH2BN_MEDIAN CH2DN_MEAN RAT2N_MEAN CH2IN_MEDIAN CH2DN_MEDIAN RAT1N_MEAN RAT2N_MEDIAN LOG_RAT2N_MEAN VALUE
1 9981 268 9873 253 108 15 9611 258 9970 356 -262 5 0 0 2725 90 1318 825 8 0 3 0 123 -257 7.2 .139 null .065 .089 4.976 156 975 .006 .11 150 2600 9930 29 44 20 35 0 283 267 16 .147 272 5 6.822 null -2.77 null
2 16369 2691 9936 287 6433 2404 10031 2462 10486 1328 95 2175 0 0 14720 956 3121 2931 45 23 39 0 8837 2270 2.676 .374 22.895 .235 .198 2.436 208 933 .089 .4 160 2800 9920 28 44 40 56 0 2840 303 2537 .394 2598 2295 2.536 24.163 -1.342 4.595
3 19971 14143 9602 336 10369 13807 13992 14513 10791 2069 4390 14177 0 0 12843 1495 4826 3422 48 100 33 100 24176 18567 .751 1.332 3.229 1.975 2.029 3.547 156 858 .515 .49 150 3010 9910 27 42 61 76 0 14926 355 14572 1.405 15317 14962 .712 3.408 .491 1.769
4 18974 2922 9408 319 9566 2603 14570 2520 10102 2490 5162 2201 0 0 13505 1530 3764 5083 52 8 43 0 12169 7363 3.675 .272 .426 .288 .214 3.293 208 1026 .128 .26 170 3190 9920 27 44 78 95 0 3084 337 2747 .287 2660 2323 3.482 .45 -1.8 -1.152
5 19390 12241 8591 320 10799 11921 14914 12470 8872 1796 6323 12150 0 0 11654 2151 2182 4579 62 97 55 92 22720 18473 .906 1.104 1.922 1.65 .856 4.686 208 901 .524 .62 160 3410 9920 28 44 101 117 0 12919 338 12581 1.165 13161 12823 .858 2.028 .22 1.02
6 16997 5918 8009 358 8988 5560 13420 5479 8189 1146 5411 5121 0 0 13059 2808 1922 1713 57 92 53 81 14548 10532 1.617 .619 .946 .485 .403 2.284 156 713 .253 .63 140 3600 9920 29 43 121 135 0 6246 378 5868 .653 5782 5405 1.532 .999 -.615 -.002
7 14968 3814 8078 336 6890 3478 10885 3677 8580 1001 2807 3341 0 0 10554 1740 3279 1728 48 83 40 47 10368 6148 1.981 .505 1.19 .401 .344 3.25 256 1154 .222 .65 180 3800 9910 26 44 139 157 0 4025 355 3671 .533 3881 3526 1.877 1.256 -.908 .329
8 15349 15565 7791 357 7558 15208 14450 15716 8383 748 6659 15359 0 0 5329 2567 3623 1459 68 100 44 100 22766 22018 .497 2.012 2.307 2.688 2.309 2.599 208 857 1.731 .61 170 4010 9920 27 44 160 177 0 16427 377 16050 2.124 16586 16210 .471 2.434 1.087 1.283
9 28721 5060 7191 384 21530 4676 26920 5067 7529 562 19729 4683 0 0 15718 1302 2554 765 90 100 82 99 26206 24412 4.604 .217 .237 .288 .225 2.719 156 616 .123 .72 140 4220 9940 31 45 183 197 0 5340 405 4935 .229 5348 4942 4.363 .251 -2.125 -1.997
10 22207 5483 7142 359 15065 5124 20081 5568 7425 422 12939 5209 0 0 11999 1152 2075 259 86 100 77 100 20189 18148 2.94 .34 .403 .499 .364 3.105 156 692 .172 .67 150 4410 9930 29 44 201 216 0 5787 379 5408 .359 5876 5497 2.786 .425 -1.478 -1.235
11 16213 9944 7163 380 9050 9564 14487 10606 7276 427 7324 10226 0 0 7071 2367 1165 240 90 100 81 99 18614 17550 .946 1.057 1.396 1.483 1.15 3.097 208 725 .708 .72 160 4610 9930 29 45 221 237 0 10495 401 10094 1.115 11193 10792 .897 1.474 .157 .559
12 19151 12124 6815 431 12336 11693 16197 12386 6888 491 9382 11955 0 0 8556 1834 1120 270 98 100 93 100 24029 21337 1.055 .948 1.274 1.243 1.199 2.315 208 725 .644 .73 170 4810 9930 28 45 240 257 0 12795 455 12341 1 13072 12617 1 1.345 .001 .427
13 10756 9255 6797 468 3959 8787 10234 9267 6885 630 3437 8799 0 0 3066 1030 1077 772 89 100 73 100 12746 12236 .451 2.219 2.56 2.719 2.527 2.121 256 876 1.868 .64 180 5000 9930 28 46 259 277 0 9767 494 9274 2.342 9780 9286 .427 2.702 1.228 1.434
14 10760 11526 6915 475 3845 11051 9368 11634 7021 658 2453 11159 0 0 3860 1598 1055 774 69 100 52 100 14896 13612 .348 2.874 4.549 3.624 2.78 3.149 256 931 2.831 .48 190 5220 9930 27 46 280 299 0 12164 501 11663 3.033 12278 11777 .33 4.801 1.601 2.263
15 10949 16231 6788 542 4161 15689 10746 16190 6955 847 3958 15648 0 0 3184 3391 1283 1364 79 100 69 100 19850 19606 .265 3.77 3.954 4.553 3.52 3.248 208 725 4.367 .52 170 5410 9930 28 45 300 317 0 17130 572 16558 3.979 17087 16515 .251 4.172 1.993 2.061
16 11374 10573 6215 554 5159 10019 10774 10311 6452 800 4559 9757 0 0 3467 1677 1628 1262 84 100 68 100 15178 14316 .515 1.942 2.14 2.427 2.016 2.469 256 1044 1.65 .66 190 5610 9920 26 45 319 338 0 11158 585 10574 2.05 10882 10297 .488 2.259 1.035 1.175
17 20739 4252 5797 544 14942 3708 20085 4263 5960 743 14288 3719 0 0 11400 1563 1592 1154 86 94 77 76 18650 18007 4.03 .248 .26 .326 .248 2.975 208 788 .151 .71 160 5800 9920 28 44 340 356 0 4487 574 3913 .262 4499 3925 3.818 .275 -1.933 -1.864
18 26088 4904 5661 490 20427 4414 25708 4973 5716 535 20047 4483 0 0 13264 1162 805 264 93 100 92 100 24841 24530 4.628 .216 .224 .25 .204 2.123 208 1182 .144 .79 170 6020 9920 27 44 361 378 0 5176 517 4658 .228 5248 4731 4.385 .236 -2.133 -2.083
19 12557 352 9643 309 2914 43 10058 296 9766 440 415 -13 0 0 6256 170 1522 743 26 0 26 0 2957 402 67.767 .015 null .04 .044 4.056 52 307 .016 .54 80 2620 10120 52 60 26 34 0 371 326 45 .016 312 -14 64.212 null -6.005 null
20 12193 10982 10676 458 1517 10524 10723 10880 11702 2858 47 10422 0 0 4633 1703 4045 4280 15 100 8 88 12041 10469 .144 6.937 221.745 5.45 3.84 5.092 156 670 23.447 .03 150 2810 10120 48 63 41 56 0 11590 483 11107 7.322 11482 10999 .137 234.024 2.872 7.871

Total number of rows: 4992

Table truncated, full table size 1210 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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