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Sample GSM184227 Query DataSets for GSM184227
Status Public on Aug 09, 2007
Title mk291a5-3
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 mk291a5-3
Organism Helicobacter pylori
Characteristics 500 ng mk291a5-3
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 = 1920, 9080; 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 = 31.51; Parameter Scan Time = 10:36:52; Parameter PMT Volts = 610; Parameter Scan Date = 2004-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 54984; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.60; Parameter Scan Power = 100; 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 = 31.51; Parameter Scan Time = 10:36:52; Parameter PMT Volts = 620; Parameter Scan Date = 2004-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 54659; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [92865]; Parameter Laser Power = 3.75; Parameter Scanning software version = 2.0.3.1; 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/2004-12/58093.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
1 418 312 436 322 -18 -10 414 308 450 329 -22 -14 0 0 117 134 144 122 8 10 0 3 -28 -36 null null null 1.255 1.224 4.092 156 897 .07 .03 150 2430 9450 29 44 43 58 0 267 275 -9 null 263 -12 null null null null
2 3235 3386 441 326 2794 3060 3153 3410 458 340 2712 3084 0 0 889 1105 153 166 100 99 100 99 5854 5796 .913 1.095 1.137 1.069 1.092 1.385 208 697 1.124 .93 160 2630 9460 30 46 63 79 0 2896 279 2618 .937 2917 2638 1.067 .973 -.094 -.04
3 11461 15059 449 340 11012 14719 11660 15655 797 558 11211 15315 0 0 3164 4320 2148 1720 99 99 98 99 25731 26526 .748 1.337 1.366 1.335 1.334 1.249 208 811 1.356 .96 170 2820 9450 28 45 81 98 0 12882 291 12591 1.143 13392 13101 .875 1.169 .193 .225
4 4192 4336 471 363 3721 3973 4072 4155 1010 883 3601 3792 0 0 1267 1306 2672 2957 79 75 12 8 7694 7393 .937 1.068 1.053 1.082 1.066 1.355 208 853 1.134 .91 170 3020 9460 29 46 101 118 0 3709 311 3399 .913 3554 3244 1.095 .901 -.131 -.151
5 11010 15702 469 348 10541 15354 10908 15529 734 697 10439 15181 0 0 2540 4048 1381 1810 100 100 100 100 25895 25620 .687 1.457 1.454 1.45 1.452 1.194 208 755 1.489 .97 160 3230 9460 30 46 123 139 0 13432 298 13134 1.246 13284 12986 .803 1.244 .317 .315
6 4922 5066 473 338 4449 4728 4979 5084 651 503 4506 4746 0 0 1919 2155 1179 1174 92 92 84 86 9177 9252 .941 1.063 1.053 1.037 1.045 1.343 156 604 1.088 .96 140 3410 9460 31 45 142 156 0 4334 289 4044 .909 4349 4060 1.1 .901 -.138 -.15
7 3514 3234 466 346 3048 2888 3586 3476 511 384 3120 3130 0 0 2334 2191 255 208 90 89 78 81 5936 6250 1.055 .948 1.003 .941 .949 1.824 208 802 .968 .95 170 3630 9470 30 47 162 179 0 2766 296 2470 .811 2973 2677 1.234 .858 -.303 -.221
8 14789 15208 469 351 14320 14857 14872 15190 507 375 14403 14839 0 0 3906 4361 236 166 100 100 100 100 29177 29242 .964 1.038 1.03 1.031 1.04 1.292 208 861 1.053 .96 170 3830 9460 29 46 182 199 0 13009 300 12709 .888 12994 12694 1.127 .881 -.172 -.182
9 6933 7024 475 354 6458 6670 7588 7266 514 374 7113 6912 0 0 3561 3644 236 158 94 98 94 97 13128 14025 .968 1.033 .972 1.097 1.016 1.876 156 694 1.036 .94 140 4030 9450 30 44 204 218 0 6009 303 5706 .884 6216 5913 1.132 .831 -.179 -.267
10 5922 6409 483 368 5439 6041 6046 6718 528 391 5563 6350 0 0 2129 2176 251 165 100 100 100 100 11480 11913 .9 1.111 1.141 1.129 1.139 1.324 156 743 1.083 .95 150 4210 9460 30 45 221 236 0 5482 315 5168 .95 5747 5432 1.053 .976 -.074 -.034
11 7949 8723 470 382 7479 8341 8081 8988 556 431 7611 8606 0 0 1955 1901 421 345 100 100 100 100 15820 16217 .897 1.115 1.131 1.129 1.117 1.262 156 775 1.089 .96 150 4430 9450 29 44 243 258 0 7462 327 7135 .954 7689 7362 1.048 .967 -.068 -.048
12 10223 14977 475 371 9748 14606 10947 15902 543 418 10472 15531 0 0 2988 4731 376 328 100 100 100 100 24354 26003 .667 1.498 1.483 1.493 1.505 1.209 208 937 1.518 .98 170 4630 9450 28 45 262 279 0 12812 317 12494 1.282 13603 13286 .78 1.269 .358 .343
13 9974 14102 467 361 9507 13741 10300 14396 504 381 9833 14035 0 0 2154 3472 207 178 100 100 100 100 23248 23868 .692 1.445 1.427 1.437 1.421 1.196 256 1084 1.484 .97 190 4840 9450 27 46 282 301 0 12063 309 11754 1.236 12315 12006 .809 1.221 .306 .288
14 6537 11388 459 349 6078 11039 6916 11758 494 371 6457 11409 0 0 2465 4245 222 215 99 100 99 100 17117 17866 .551 1.816 1.767 1.883 1.832 1.509 256 929 1.803 .97 180 5020 9450 28 46 301 319 0 9742 299 9443 1.554 10058 9760 .644 1.511 .636 .596
15 8737 20813 457 359 8280 20454 8769 20501 500 406 8312 20142 0 0 2575 7372 269 361 100 100 100 100 28734 28454 .405 2.47 2.423 2.426 2.486 1.32 208 738 2.595 .96 170 5230 9460 29 46 322 339 0 17804 307 17497 2.113 17537 17230 .473 2.073 1.079 1.052
16 11589 13913 458 372 11131 13541 11444 13819 493 396 10986 13447 0 0 3431 4394 227 280 100 100 100 100 24672 24433 .822 1.217 1.224 1.212 1.228 1.365 256 973 1.229 .97 180 5420 9450 28 46 341 359 0 11902 318 11583 1.041 11821 11503 .961 1.047 .057 .066
17 7304 9067 452 352 6852 8715 7567 9576 497 388 7115 9224 0 0 3763 4745 301 302 99 99 97 97 15567 16339 .786 1.272 1.296 1.259 1.279 1.482 208 831 1.29 .95 170 5630 9450 28 45 362 379 0 7756 301 7455 1.088 8192 7890 .919 1.109 .122 .149
18 7979 10868 453 326 7526 10542 8862 11606 499 371 8409 11280 0 0 3019 3884 300 308 99 100 97 100 18068 19689 .714 1.401 1.341 1.482 1.394 1.499 208 1008 1.388 .96 160 5830 9460 30 46 383 399 0 9297 279 9018 1.198 9928 9649 .835 1.147 .261 .198
19 446 340 442 322 4 18 423 329 458 332 -19 7 0 0 151 112 152 131 14 16 1 3 22 -12 .222 4.5 null .606 .576 3.401 156 695 .138 .03 150 2430 9650 49 64 43 58 0 291 275 15 3.849 281 6 .26 null 1.945 null
20 13036 13233 476 347 12560 12886 13703 13960 788 506 13227 13613 0 0 3458 4161 1983 1171 100 100 99 98 25446 26840 .975 1.026 1.029 .998 1.029 1.236 256 494 1.048 .97 180 2640 9650 48 66 63 81 0 11320 297 11023 .878 11942 11645 1.139 .88 -.188 -.184

Total number of rows: 4992

Table truncated, full table size 1224 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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