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Sample GSM91123 Query DataSets for GSM91123
Status Public on Jan 07, 2006
Title PMSS200_array 1
Sample type genomic
 
Channel 1
Source name 1 ug Tigr genomic DNA + 1 ug Astra genomic DNA
Organism Helicobacter pylori
Characteristics 1 ug Tigr genomic DNA + 1 ug Astra genomic DNA
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name 2 ug premouse SS2000 genomic DNA
Organism Helicobacter pylori
Characteristics 2 ug premouse SS2000 genomic DNA
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Genomic DNA, Strain Comparison
Image: http://smd.stanford.edu/MicroArray/gifs/2000-06/6829.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 7340 6411 489 227 6851 6184 null null 499 238 null null null null null null null null 100 98 null null null null 1.108 .903 null null .871 null 52 288 .893 .94 null null null 73 81 40 48 0 7203 255 6948 1.014 null null .986 null .02 null .02
2 3181 2984 480 226 2701 2758 null null 486 232 null null null null null null null null 86 94 null null null null .979 1.021 null null .902 null 52 332 .956 .87 null null null 72 80 64 72 0 3352 253 3099 1.147 null null .872 null .198 null .198
3 4472 3166 523 232 3949 2934 null null 541 247 null null null null null null null null 81 78 null null null null 1.346 .743 null null .626 null 32 160 .709 .86 null null null 72 78 91 97 0 3557 260 3297 .835 null null 1.198 null -.26 null -.26
4 438 199 440 200 null null null null 453 212 null null null null null null null null 12 8 null null null null null null null null .586 null 80 552 .113 .19 null null null 71 81 114 124 -100 223 224 null null null null null null null null
5 425 186 434 189 null null null null 439 195 null null null null null null null null 20 13 null null null null null null null null .522 null 80 552 .023 .04 null null null 71 81 138 148 -100 208 212 null null null null null null null null
6 2330 901 451 189 1879 712 null null 462 195 null null null null null null null null 100 100 null null null null 2.639 .379 null null .388 null 32 230 .333 .83 null null null 71 78 162 169 0 1012 212 800 .426 null null 2.349 null -1.232 null -1.232
7 79 69 114 93 null null null null 225 118 null null null null null null null null 0 0 null null null null null null null null .745 null 80 552 .287 .41 null null null 71 81 186 196 -100 77 104 null null null null null null null null
8 814 313 514 213 300 100 null null 517 221 null null null null null null null null 53 53 null null null null 3 .333 null null .389 null 32 160 .243 .66 null null null 72 78 211 217 -100 351 239 112 .373 null null 2.679 null null -1.421
9 120 103 469 187 null null null null 459 191 null null null null null null null null 0 3 null null null null null null null null .292 null 80 544 .264 .73 null null null 70 80 234 244 -100 115 210 null null null null null null null null
10 392 192 426 163 null 29 null null 375 172 null null null null null null null null 7 25 null null null null null null null null .362 null 80 552 .301 .75 null null null 70 80 258 268 -100 215 183 32 null null null null null null null
11 530 233 439 164 91 69 null null 382 163 null null null null null null null null 16 38 null null null null 1.319 .758 null null .639 null 80 552 .263 .66 null null null 70 80 282 292 -100 261 184 77 .846 null null 1.182 null null -.241
12 6597 652 523 208 6074 444 null null 539 212 null null null null null null null null 100 96 null null null null 13.68 .073 null null .079 null 32 230 .066 .81 null null null 71 78 308 315 0 732 233 499 .082 null null 12.172 null -3.606 null -3.606
13 1454 855 542 236 912 619 null null 544 240 null null null null null null null null 87 87 null null null null 1.473 .679 null null .773 null 32 220 .548 .84 null null null 70 77 331 338 -100 960 265 695 .762 null null 1.312 null null -.392
14 3820 2346 560 236 3260 2110 null null 567 241 null null null null null null null null 100 100 null null null null 1.545 .647 null null .721 null 32 170 .609 .91 null null null 72 78 357 363 0 2635 265 2370 .727 null null 1.376 null -.46 null -.46
15 1962 1356 556 237 1406 1119 null null 552 238 null null null null null null null null 100 100 null null null null 1.256 .796 null null .823 null 12 90 .702 .8 null null null 71 76 380 385 -100 1523 266 1257 .894 null null 1.119 null null -.162
16 611 301 528 211 83 90 null null 545 219 null null null null null null null null 30 46 null null null null .922 1.084 null null .865 null 80 552 .317 .41 null null null 70 80 403 413 -100 338 237 101 1.217 null null .822 null null .283
17 1569 895 528 227 1041 668 null null 531 229 null null null null null null null null 96 100 null null null null 1.558 .642 null null .648 null 32 170 .569 .88 null null null 72 78 429 435 -100 1005 255 750 .72 null null 1.388 null null -.473
18 1087 677 512 243 575 434 null null 515 252 null null null null null null null null 90 90 null null null null 1.325 .755 null null .632 null 32 176 .604 .79 null null null 97 103 46 52 0 760 273 487 .847 null null 1.181 null -.24 null -.24
19 2605 1901 519 251 2086 1650 null null 535 260 null null null null null null null null 98 94 null null null null 1.264 .791 null null .748 null 52 340 .776 .92 null null null 95 103 69 77 0 2135 282 1853 .888 null null 1.126 null -.171 null -.171
20 522 264 519 255 3 9 null null 531 259 null null null null null null null null 17 20 null null null null .333 3 null null .572 null 80 560 .151 .28 null null null 95 105 91 101 -100 296 286 10 3.333 null null .3 null null 1.737

Total number of rows: 4608

Table truncated, full table size 1147 Kbytes.




Supplementary data files not provided
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