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Sample GSM91126 Query DataSets for GSM91126
Status Public on Jan 07, 2006
Title 10700_array 2
Sample type genomic
 
Channel 1
Source name 0.7 ug Tigr genomic DNA + 0.7 ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 0.7 ug Tigr genomic DNA + 0.7 ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug 10700(ss1 premouse) genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug 10700(ss1 premouse) genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-05/5365.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 06, 2006
Last update date Sep 22, 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 (2)
GSE3479 Helicobacter pylori bacterial populations
GSE3988 Chronic Helicobacter pylori Infection with Sydney Strain 1 and Mouse-Adapted Sydney Strain 2000

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE same as UNF_VALUE but with flagged values removed
LOG_RAT2N_MEDIAN 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
UNF_VALUE 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

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 VALUE LOG_RAT2N_MEDIAN UNF_VALUE
1 6211 6375 438 2446 5773 3929 null null 447 2452 null null null null null null null null 100 94 null null null null 1.469 .681 null null .641 null 52 320 .689 .88 null null null 37 45 122 130 0 7244 2779 4465 .773 null null 1.293 null -.371 null -.371
2 4833 2627 462 2426 4371 201 null null 516 2433 null null null null null null null null 96 21 null null null null 21.746 .046 null null .122 null 32 176 .152 .54 null null null 39 45 146 152 0 2985 2756 229 .052 null null 19.087 null -4.255 null -4.255
3 3282 4997 507 2352 2775 2645 null null 560 2398 null null null null null null null null 100 83 null null null null 1.049 .953 null null 1.14 null 12 104 .853 .81 null null null 38 43 173 178 0 5678 2672 3006 1.083 null null .923 null .115 null .115
4 470 2203 451 2351 19 null null null 455 2403 null null null null null null null null 23 16 null null null null null null null null 7.872 null 80 552 .082 0 null null null 35 45 193 203 -100 2503 2671 null null null null null null null null
5 475 2275 454 2403 21 null null null 462 2430 null null null null null null null null 23 16 null null null null null null null null 5.956 null 80 552 .586 .1 null null null 35 45 217 227 -100 2585 2730 null null null null null null null null
6 3022 3033 474 2437 2548 596 null null 475 2499 null null null null null null null null 100 59 null null null null 4.275 .234 null null .445 null 32 170 .243 .51 null null null 37 43 244 250 0 3446 2769 677 .266 null null 3.764 null -1.912 null -1.912
7 571 2207 471 2426 100 null null null 474 2460 null null null null null null null null 35 11 null null null null null null null null 3.971 null 80 552 .479 .15 null null null 34 44 265 275 -100 2507 2756 null null null null null null null null
8 542 2200 457 2506 85 null null null 462 2519 null null null null null null null null 30 15 null null null null null null null null 5.617 null 80 552 .947 .27 null null null 34 44 289 299 -100 2500 2847 null null null null null null null null
9 2265 3721 470 2516 1795 1205 null null 477 2579 null null null null null null null null 93 65 null null null null 1.49 .671 null null .981 null 32 176 .745 .77 null null null 38 44 315 321 0 4228 2859 1369 .763 null null 1.311 null -.391 null -.391
10 526 2158 470 2444 56 null null null 470 2458 null null null null null null null null 35 3 null null null null null null null null 4.625 null 80 552 null 0 null null null 34 44 337 347 -100 2452 2777 null null null null null null null null
11 542 2274 451 2492 91 null null null 457 2503 null null null null null null null null 37 7 null null null null null null null null 4.343 null 80 552 .005 0 null null null 34 44 361 371 -100 2584 2831 null null null null null null null null
12 6728 2257 474 2433 6254 null null null 479 2468 null null null null null null null null 100 18 null null null null null null null null .084 null 32 176 null null null null null 36 42 388 394 0 2564 2764 null null null null null null null null null
13 1235 2495 449 2519 786 null null null 454 2555 null null null null null null null null 70 13 null null null null null null null null .514 null 80 552 .134 .16 null null null 33 43 409 419 -100 2835 2862 null null null null null null null null
14 3094 5596 479 2484 2615 3112 null null 489 2532 null null null null null null null null 93 87 null null null null .84 1.19 null null 1.352 null 32 236 1.104 .84 null null null 35 42 434 441 0 6359 2822 3537 1.353 null null .739 null .436 null .436
15 673 2524 446 2539 227 null null null 449 2534 null null null null null null null null 53 26 null null null null null null null null 2.683 null 80 552 .375 .19 null null null 33 43 457 467 -100 2868 2885 null null null null null null null null
16 625 2456 442 2518 183 null null null 456 2716 null null null null null null null null 31 0 null null null null null null null null 3.087 null 80 552 9.508 .82 null null null 33 43 481 491 -100 2790 2861 null null null null null null null null
17 2855 4024 448 2632 2407 1392 null null 457 2635 null null null null null null null null 91 66 null null null null 1.729 .578 null null .886 null 12 104 .688 .72 null null null 35 40 508 513 0 4572 2990 1582 .657 null null 1.521 null -.605 null -.605
18 1741 3286 440 2279 1301 1007 null null 447 2318 null null null null null null null null 100 57 null null null null 1.292 .774 null null .971 null 12 104 .771 .67 null null null 61 66 124 129 0 3734 2589 1145 .88 null null 1.136 null -.184 null -.184
19 1574 3121 458 2343 1116 778 null null 462 2381 null null null null null null null null 92 59 null null null null 1.434 .697 null null .816 null 52 340 .696 .58 null null null 61 69 147 155 0 3546 2662 884 .792 null null 1.262 null -.336 null -.336
20 483 2110 463 2342 20 null null null 465 2400 null null null null null null null null 25 11 null null null null null null null null 5.455 null 80 560 .338 .06 null null null 59 69 169 179 -100 2397 2661 null null null null null null null null

Total number of rows: 4608

Table truncated, full table size 1158 Kbytes.




Supplementary data files not provided

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