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Sample GSM72956 Query DataSets for GSM72956
Status Public on Aug 31, 2005
Title C6
Sample type RNA
 
Channel 1
Source name pooled aged matched control samples
Organism Mus musculus
Characteristics pooled aged matched control samples
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name gastric biopsy JO11 C6
Organism Mus musculus
Characteristics gastric biopsy JO11 C6
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29647.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 Aug 30, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
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 GPL2727
Series (2)
GSE3237 Role of antigenic drive in pathogenesis of MALT lymphoma
GSE3648 Histopathological stages of disease in Helicobacter-induced mucosa-associated lymphoid tissue lymphoma.

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
1 964 1882 276 129 688 1753 930 1920 277 141 654 1791 0 0 563 1208 45 74 84 90 80 90 2441 2445 .392 2.548 2.739 2.431 2.441 2.776 120 519 2.472 .93 120 1640 9410 71 83 70 82 0 1046 72 974 1.416 1067 995 .706 1.521 .501 .605
2 1243 2437 281 134 962 2303 1306 2554 286 148 1025 2420 0 0 627 1234 56 81 84 98 84 96 3265 3445 .418 2.394 2.361 2.598 2.489 2.097 52 243 2.43 .87 90 1780 9400 71 80 85 94 0 1354 74 1279 1.33 1419 1344 .752 1.312 .411 .391
3 891 1647 283 134 608 1513 887 1583 287 143 604 1449 0 0 497 1032 46 59 85 90 80 87 2121 2053 .402 2.488 2.399 2.196 2.406 2.771 80 350 2.458 .91 100 1930 9410 72 82 100 110 0 915 74 841 1.382 879 805 .723 1.333 .467 .414
4 656 1174 280 136 376 1038 625 1033 285 161 345 897 0 0 254 680 52 139 90 94 86 90 1414 1242 .362 2.761 2.6 2.66 2.656 1.608 52 299 2.965 .85 90 2070 9390 70 79 114 123 0 652 76 577 1.534 574 498 .652 1.444 .617 .531
5 713 1270 280 141 433 1129 718 1296 289 176 438 1155 0 0 339 738 70 198 85 87 82 78 1562 1593 .384 2.607 2.637 2.339 2.547 2.32 80 387 2.505 .89 100 2210 9400 71 81 128 138 0 706 78 627 1.449 720 642 .69 1.465 .535 .551
6 936 1775 277 139 659 1636 994 1797 282 161 717 1658 0 0 410 837 66 164 87 93 85 90 2295 2375 .403 2.483 2.312 2.103 2.357 2.293 80 416 2.381 .87 110 2370 9410 71 82 143 154 0 986 77 909 1.379 998 921 .725 1.285 .464 .361
7 868 1510 263 131 605 1379 881 1508 268 148 618 1377 0 0 328 627 51 90 96 98 92 98 1984 1995 .439 2.279 2.228 2.254 2.373 1.922 52 303 2.418 .84 90 2510 9390 70 79 158 167 0 839 73 766 1.266 838 765 .79 1.238 .341 .308
8 742 1329 268 123 474 1206 774 1390 270 137 506 1267 0 0 332 586 46 75 84 96 84 96 1680 1773 .393 2.544 2.504 2.329 2.374 1.862 52 317 2.366 .91 90 2650 9400 71 80 172 181 0 738 68 670 1.414 772 704 .707 1.391 .499 .476
9 819 1108 283 131 536 977 826 1112 293 156 543 981 0 0 245 423 58 106 94 98 94 94 1513 1524 .549 1.823 1.807 1.766 1.742 1.379 52 326 1.847 .9 90 2800 9390 70 79 187 196 0 616 73 543 1.013 618 545 .988 1.004 .018 .005
10 438 454 290 143 148 311 380 234 296 151 90 91 0 0 316 463 45 65 59 53 50 40 459 181 .476 2.101 1.011 .989 1.107 3.275 32 160 1.959 .68 60 2950 9410 74 80 204 210 0 252 79 173 1.167 130 51 .857 .562 .223 -.832
11 595 753 295 138 300 615 566 702 298 151 271 564 0 0 296 463 47 76 80 86 73 78 915 835 .488 2.05 2.081 1.507 1.653 3.37 80 397 2.042 .79 100 3100 9410 72 82 217 227 0 418 77 342 1.139 390 313 .878 1.156 .188 .209
12 701 918 299 147 402 771 663 912 307 179 364 765 0 0 216 347 63 118 93 96 90 96 1173 1129 .521 1.918 2.102 2.06 1.847 1.893 32 172 1.792 .87 60 3250 9390 72 78 234 240 0 510 82 428 1.066 507 425 .939 1.168 .092 .224
13 719 952 286 130 433 822 703 919 293 148 417 789 0 0 161 300 48 71 100 100 100 100 1255 1206 .527 1.898 1.892 1.88 1.905 1.694 32 176 1.829 .85 60 3390 9390 72 78 248 254 0 529 72 457 1.055 511 438 .948 1.051 .077 .072
14 855 1218 292 141 563 1077 860 1244 298 173 568 1103 0 0 233 520 65 116 100 100 100 100 1640 1671 .523 1.913 1.942 1.808 2.056 1.723 32 217 2.163 .84 70 3530 9380 70 77 261 268 0 677 78 598 1.063 691 613 .941 1.079 .088 .109
15 501 386 292 138 209 248 504 356 297 155 212 218 0 0 76 203 57 88 96 81 87 62 457 430 .843 1.187 1.028 .983 1.17 1.904 32 228 1.253 .67 70 3670 9390 71 78 275 282 0 214 77 138 .659 198 121 1.517 .571 -.601 -.808
16 622 648 287 140 335 508 579 575 290 160 292 435 0 0 211 332 57 78 90 90 90 87 843 727 .659 1.516 1.49 1.421 1.544 2.742 32 232 1.605 .84 70 3810 9380 70 77 289 296 0 360 78 282 .842 319 242 1.187 .828 -.247 -.273
17 580 621 268 133 312 488 547 550 265 141 279 417 0 0 141 243 56 46 100 100 100 100 800 696 .639 1.564 1.495 1.546 1.807 1.466 12 68 1.476 .8 40 3960 9400 74 78 306 310 0 345 74 271 .869 306 232 1.151 .83 -.203 -.268
18 893 905 279 146 614 759 919 900 280 163 640 754 0 0 125 241 62 81 100 100 100 100 1373 1394 .809 1.236 1.178 1.206 1.207 1.287 12 104 1.333 .87 50 4110 9390 72 77 320 325 0 503 81 422 .687 500 419 1.456 .655 -.542 -.612
19 621 547 265 127 356 420 618 547 258 132 353 420 0 0 184 201 57 50 100 100 91 91 776 773 .848 1.18 1.19 1.15 1.22 1.65 12 104 1.284 .83 50 4260 9390 72 77 335 340 0 304 71 233 .655 304 233 1.526 .661 -.609 -.597
20 600 622 280 136 320 486 601 625 281 141 321 489 0 0 191 219 39 44 90 100 87 96 806 810 .658 1.519 1.523 1.48 1.381 2.217 32 176 1.367 .82 60 4410 9390 72 78 350 356 0 346 76 270 .844 347 272 1.185 .846 -.245 -.241

Total number of rows: 42624

Table truncated, full table size 9163 Kbytes.




Supplementary data files not provided
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