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Sample GSM184260 Query DataSets for GSM184260
Status Public on Aug 09, 2007
Title OVX-34 vs 26695/J99 mix-2
Sample type genomic
 
Channel 1
Source name 0.25 ug 26695 + 0.25 ug j99 genomic DNA
Organism Helicobacter pylori
Characteristics 0.25 ug 26695 + 0.25 ug j99 genomic DNA
Extracted molecule genomic DNA
Extraction protocol not provided
Label Cy3
Label protocol not provided
 
Channel 2
Source name 0.5 ug genomic DNA OVX-34
Organism Helicobacter pylori
Characteristics 0.5 ug genomic DNA OVX-34
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 = 2040, 8560; 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 = 31.73; Parameter Scan Time = 09:21:15; Parameter PMT Volts = 630; Parameter Scan Date = 2006-06-14; Parameter Pixel Size = 10; Parameter Laser on time = 87026; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.49; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.3.2; 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 = 31.73; Parameter Scan Time = 09:21:15; Parameter PMT Volts = 890; Parameter Scan Date = 2006-06-14; Parameter Pixel Size = 10; Parameter Laser on time = 87452; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.59; Parameter Scanning software version = 2.0.3.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Nina,,Salama
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2006-06/68912.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 GPL5124
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
1 899 907 358 438 541 469 841 827 537 604 483 389 0 0 355 455 474 559 51 35 10 7 1010 872 1.154 .867 .805 .951 .845 3.666 156 1113 1.314 .56 150 2610 9710 107 122 49 64 0 1235 597 639 1.181 1126 530 .847 1.097 .24 .134
2 1729 1824 305 373 1424 1451 1558 1661 427 509 1253 1288 0 0 745 932 364 470 99 87 81 66 2875 2541 .981 1.019 1.028 .904 1.015 2.389 208 1282 1.182 .7 170 2870 9710 106 123 74 91 0 2484 508 1976 1.388 2262 1754 .721 1.4 .473 .486
3 12871 11682 251 279 12620 11403 13980 12322 276 340 13729 12043 0 0 4451 3722 133 278 99 100 99 100 24023 25772 1.107 .904 .877 .951 .905 1.611 208 1163 .885 .95 170 3140 9710 106 123 101 118 0 15912 380 15532 1.231 16783 16403 .813 1.195 .299 .257
4 1693 1793 247 287 1446 1506 1563 1663 274 335 1316 1376 0 0 731 945 133 268 99 93 98 85 2952 2692 .96 1.041 1.046 .963 1.011 2.099 316 1546 1.177 .8 200 3390 9700 104 124 125 145 0 2442 391 2051 1.419 2265 1874 .705 1.424 .504 .51
5 6994 5820 242 281 6752 5539 6345 5470 290 333 6103 5189 0 0 3603 2783 529 287 96 98 93 97 12291 11292 1.219 .82 .85 .874 .815 1.8 256 1284 .779 .91 180 3650 9710 106 124 152 170 0 7927 383 7544 1.117 7450 7068 .895 1.158 .16 .212
6 4556 2972 273 312 4283 2660 4356 2674 316 374 4083 2362 0 0 2070 1558 169 300 100 99 100 97 6943 6445 1.61 .621 .578 .585 .598 1.648 256 1347 .602 .81 180 3910 9700 105 123 178 196 0 4048 425 3623 .846 3642 3217 1.182 .788 -.241 -.344
7 9276 10955 357 425 8919 10530 8598 10436 496 597 8241 10011 0 0 3104 3974 1201 1210 100 100 100 100 19449 18252 .847 1.181 1.215 1.172 1.185 1.364 208 1198 1.254 .9 170 4160 9700 105 122 203 220 0 14921 579 14343 1.608 14215 13636 .622 1.655 .685 .726
8 2719 2769 344 412 2375 2357 2616 2531 441 557 2272 2119 0 0 948 1283 726 957 98 90 83 58 4732 4391 1.008 .992 .933 .943 .943 1.751 256 1328 1.099 .82 180 4440 9700 105 123 231 249 0 3772 561 3210 1.352 3447 2886 .74 1.27 .435 .345
9 4114 4075 338 388 3776 3687 3766 3749 424 458 3428 3361 0 0 2677 2156 611 403 100 99 95 98 7463 6789 1.024 .976 .98 .963 .977 1.699 256 1333 .915 .83 180 4690 9690 104 122 256 274 0 5550 528 5022 1.33 5106 4578 .752 1.335 .411 .417
10 5247 5409 355 393 4892 5016 4854 4362 505 465 4499 3969 0 0 3338 3698 1195 341 93 100 78 99 9908 8468 .975 1.025 .882 1.013 1.033 1.698 256 1373 1.064 .87 190 4960 9700 104 123 282 301 0 7367 535 6832 1.397 5941 5406 .716 1.202 .482 .265
11 14866 14976 331 354 14535 14622 13944 14335 390 410 13613 13981 0 0 5566 5118 387 307 100 100 100 100 29157 27594 .994 1.006 1.027 1.02 .99 1.298 208 1122 .987 .95 170 5210 9700 105 122 308 325 0 20398 482 19916 1.37 19525 19043 .73 1.399 .454 .484
12 11726 12617 320 350 11406 12267 12231 11984 368 411 11911 11634 0 0 5771 5423 206 306 99 100 98 100 23673 23545 .93 1.075 .977 1.208 1.088 1.82 208 1198 1.041 .95 170 5470 9700 105 122 334 351 0 17185 477 16708 1.465 16323 15846 .683 1.33 .551 .412
13 14098 8570 365 396 13733 8174 14810 8760 417 476 14445 8364 0 0 4605 2170 229 370 100 100 100 100 21907 22809 1.68 .595 .579 .614 .606 1.442 208 1212 .55 .92 170 5720 9690 104 121 359 376 0 11673 539 11134 .811 11932 11392 1.233 .789 -.303 -.343
14 7299 4672 416 473 6883 4199 7179 4256 504 581 6763 3783 0 0 3784 2700 606 678 99 98 96 94 11082 10546 1.639 .61 .559 .614 .607 1.702 256 1265 .604 .83 180 5990 9690 104 122 386 404 0 6364 644 5719 .831 5797 5153 1.203 .762 -.267 -.392
15 16021 15017 442 509 15579 14508 14745 13620 585 679 14303 13111 0 0 7880 7535 1052 1031 99 98 95 96 30087 27414 1.074 .931 .917 .92 .936 1.422 256 1241 .929 .94 180 6240 9690 104 122 411 429 0 20454 693 19761 1.268 18551 17858 .788 1.249 .343 .32
16 14500 12707 417 537 14083 12170 14569 12947 584 1086 14152 12410 0 0 5881 4577 1284 4496 100 94 99 72 26253 26562 1.157 .864 .877 .873 .86 1.39 208 1332 .842 .94 170 6500 9690 104 121 437 454 0 17308 731 16576 1.177 17635 16903 .85 1.194 .235 .256
17 7798 5290 323 394 7475 4896 8420 5243 435 522 8097 4849 0 0 2617 1956 365 487 100 99 99 98 12371 12946 1.527 .655 .599 .657 .644 1.567 208 1185 .646 .9 170 2630 9960 131 148 50 67 0 7205 537 6669 .892 7141 6605 1.121 .816 -.165 -.294
18 6744 6564 299 350 6445 6214 6080 5741 346 451 5781 5391 0 0 3766 4419 198 396 100 99 100 99 12659 11172 1.037 .964 .933 .9 .933 1.686 208 992 1.053 .86 170 2870 9950 130 147 74 91 0 8941 477 8464 1.313 7820 7343 .761 1.27 .393 .345
19 4507 4747 274 311 4233 4436 4045 4207 299 381 3771 3896 0 0 2791 2734 124 307 99 98 98 96 8669 7667 .954 1.048 1.033 1.082 1.084 1.709 256 1073 1.022 .91 180 3130 9960 131 149 100 118 0 6466 424 6042 1.427 5730 5307 .701 1.407 .513 .493
20 4495 4824 268 316 4227 4508 3499 3815 301 382 3231 3499 0 0 2663 2804 146 323 100 100 100 99 8735 6730 .938 1.066 1.083 1.026 1.076 1.537 208 1003 1.074 .89 170 3390 9950 130 147 126 143 0 6571 430 6140 1.453 5196 4766 .688 1.475 .539 .561

Total number of rows: 4032

Table truncated, full table size 970 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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