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Sample GSM87824 Query DataSets for GSM87824
Status Public on Dec 15, 2005
Title G27pH 5 T2=60
Sample type RNA
 
Channel 1
Source name 2.0 ug starter cDNA
Organism Helicobacter pylori
Characteristics 2.0 ug starter cDNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name 2.0 ug T=60 DNA
Organism Helicobacter pylori
Characteristics 2.0 ug T=60 DNA
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Environmental conditions, Time course
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21341.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 Dec 14, 2005
Last update date Sep 26, 2006
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 GPL15
Series (1)
GSE3833 Acid exposure

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 same as UNF_VALUE but with flagged values removed
UNF_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 UNF_VALUE
1 2483 2966 422 421 2061 2545 2509 2642 431 423 2087 2221 0 0 1012 1417 91 69 100 100 100 100 4606 4308 .81 1.235 1.064 1.206 1.205 1.266 52 400 1.165 .9 90 2490 41150 42 51 92 101 0 2264 321 1943 .943 2017 1695 1.061 .812 -.085 -.3 -.3
2 2078 1986 426 436 1652 1550 1507 2284 435 437 1081 1848 0 0 1944 1000 91 77 87 93 84 84 3202 2929 1.066 .938 1.71 1.208 1.552 2.482 32 236 .576 .7 70 2730 41180 46 53 117 124 0 1516 333 1183 .716 1744 1411 1.396 1.305 -.482 .384 .384
3 1414 2358 416 433 998 1925 1454 2127 442 436 1038 1694 0 0 648 1251 143 71 93 100 84 100 2923 2732 .518 1.929 1.632 1.962 1.971 1.53 32 230 1.223 .71 70 2970 41160 44 51 141 148 0 1800 331 1469 1.472 1624 1293 .679 1.246 .558 .317 .317
4 859 656 413 427 446 229 525 441 422 426 112 14 0 0 1043 567 89 69 53 35 33 31 675 126 1.948 .513 .125 .736 .766 3.514 80 648 .508 .87 110 3200 41160 42 53 162 173 -100 501 326 175 .392 337 11 2.551 .095 -1.351 -3.39
5 630 502 427 431 203 71 460 422 436 435 33 -9 0 0 442 256 91 70 37 28 30 22 274 24 2.859 .35 null .842 1.041 3.088 80 648 .4 .57 110 3440 41170 43 54 186 197 -100 383 329 54 .267 322 null 3.745 null -1.905 null
6 1562 1060 439 451 1123 609 1216 876 458 454 777 425 0 0 1005 476 88 76 100 91 100 91 1732 1202 1.844 .542 .547 .495 .536 2.69 12 68 .428 .8 40 3680 41200 50 54 214 218 -100 809 344 465 .414 669 324 2.416 .418 -1.272 -1.26
7 1061 788 455 463 606 325 1008 769 458 462 553 306 0 0 559 347 105 73 75 62 71 62 931 859 1.865 .536 .553 .483 .468 2.191 32 176 .552 .81 60 3910 41190 48 54 236 242 0 602 353 248 .409 587 234 2.443 .422 -1.288 -1.243 -1.243
8 1206 846 483 498 723 348 849 712 491 511 366 214 0 0 972 439 109 97 82 82 71 53 1071 580 2.078 .481 .585 .665 .589 2.233 52 420 .422 .83 90 4170 41200 47 56 260 269 0 646 380 266 .367 544 163 2.722 .446 -1.444 -1.164 -1.164
9 2452 2631 476 484 1976 2147 2432 2597 474 486 1956 2113 0 0 1251 1485 93 71 98 100 96 100 4123 4069 .92 1.087 1.08 1.066 1.129 1.804 52 335 1.136 .88 80 4420 41180 46 54 286 294 0 2008 369 1639 .829 1982 1613 1.206 .825 -.27 -.278 -.278
10 795 668 446 456 349 212 563 487 457 461 117 31 0 0 706 446 95 71 52 32 37 25 561 148 1.646 .607 .265 .492 .588 3.47 80 648 .417 .76 110 4640 41180 44 55 306 317 -100 510 348 162 .464 372 24 2.157 .202 -1.109 -2.306
11 891 730 446 462 445 268 544 522 453 466 98 60 0 0 829 492 97 70 50 47 36 28 713 158 1.66 .602 .612 .597 .743 3.173 80 648 .37 .69 110 4880 41180 44 55 330 341 -100 557 353 205 .46 398 46 2.175 .467 -1.121 -1.097
12 1331 1164 471 486 860 678 1310 1102 478 487 839 616 0 0 386 400 91 74 100 98 98 98 1538 1455 1.268 .788 .734 .749 .807 1.661 52 340 .828 .87 80 5140 41210 49 57 358 366 0 889 371 518 .602 841 470 1.662 .56 -.733 -.835 -.835
13 1324 1377 457 477 867 900 906 767 461 480 449 290 0 0 814 963 102 71 98 100 84 94 1767 739 .963 1.038 .646 .924 .943 1.939 52 412 .977 .85 90 5380 41180 45 54 381 390 0 1051 364 687 .792 585 221 1.262 .493 -.336 -1.02 -1.02
14 2047 3208 463 472 1584 2736 1778 2168 466 476 1315 1696 0 0 1194 2233 94 74 100 100 98 100 4320 3011 .579 1.727 1.29 1.673 1.82 1.688 52 420 1.76 .85 90 5610 41200 47 56 404 413 0 2449 360 2089 1.319 1655 1295 .758 .985 .399 -.022 -.022
15 556 495 421 420 135 75 500 451 424 424 79 31 0 0 283 208 83 71 47 35 18 15 210 110 1.8 .556 .392 .912 .756 2.634 80 648 .562 .72 110 5850 41190 45 56 427 438 -100 378 321 57 .424 344 24 2.358 .3 -1.238 -1.739
16 1397 1944 513 505 884 1439 902 1050 983 1370 389 545 0 0 1199 2008 1736 2839 18 18 7 5 2323 934 .614 1.628 1.401 1.444 1.595 2.501 80 648 1.654 .96 110 6090 41190 45 56 451 462 -50 1484 385 1098 1.243 802 416 .805 1.069 .313 .097
17 1328 1486 501 514 827 972 948 1072 594 724 447 558 0 0 880 884 383 801 52 40 35 25 1799 1005 .851 1.175 1.248 1.311 1.303 2.054 80 656 1.638 .85 110 6330 41200 46 57 475 486 -100 1134 392 742 .897 818 426 1.115 .953 -.156 -.07
18 1071 762 433 409 638 353 825 654 438 412 392 245 0 0 528 366 93 68 93 75 84 62 991 637 1.807 .553 .625 .564 .538 2.861 32 236 .614 .88 70 2490 41400 68 75 93 100 0 582 312 269 .422 499 187 2.368 .477 -1.243 -1.068 -1.068
19 1828 2038 450 425 1378 1613 1752 1997 453 425 1302 1572 0 0 662 558 87 72 100 100 100 100 2991 2874 .854 1.171 1.207 1.183 1.337 1.431 12 68 .658 .85 40 2730 41410 71 75 119 123 0 1556 324 1231 .894 1524 1200 1.119 .922 -.162 -.118 -.118
20 1692 1221 430 425 1262 796 1259 776 441 426 829 351 0 0 1154 893 99 70 100 83 91 75 2058 1180 1.585 .631 .423 .578 .634 1.868 12 68 .721 .96 40 2970 41420 72 76 143 147 -100 932 324 608 .481 592 268 2.077 .323 -1.054 -1.629

Total number of rows: 4608

Table truncated, full table size 1089 Kbytes.




Supplementary data files not provided
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