NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM72950 Query DataSets for GSM72950
Status Public on Aug 31, 2005
Title D5
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 D5
Organism Mus musculus
Characteristics gastric biopsy JO11 D5
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29645.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 5894 10056 647 436 5247 9620 6446 10067 685 493 5799 9631 0 0 2729 5352 323 404 98 99 96 98 14867 15430 .545 1.833 1.661 1.848 1.732 1.81 120 532 1.971 .92 120 1620 9540 64 76 71 83 0 12116 525 11590 2.209 12129 11604 .453 2.001 1.143 1.001
2 9707 9477 620 284 9087 9193 9641 8423 634 310 9021 8139 0 0 6448 6161 128 173 100 98 100 97 18280 17160 .988 1.012 .902 1.078 .936 1.854 80 334 .999 .93 110 1770 9540 64 75 86 97 0 11418 342 11076 1.219 10148 9806 .82 1.087 .286 .12
3 7436 5749 620 257 6816 5492 7408 5508 639 273 6788 5251 0 0 2476 2088 153 122 100 100 100 100 12308 12039 1.241 .806 .774 .808 .764 1.375 80 367 .811 .9 110 1910 9540 64 75 100 111 0 6927 310 6617 .971 6636 6327 1.03 .932 -.043 -.102
4 4460 4588 604 252 3856 4336 5240 4513 630 262 4636 4261 0 0 2319 2367 155 83 88 96 87 95 8192 8897 .889 1.124 .919 1.258 1.011 2.25 80 353 1.038 .89 110 2050 9550 65 76 114 125 0 5528 304 5224 1.355 5437 5134 .738 1.107 .438 .147
5 5613 5895 613 265 5000 5630 4950 5597 631 281 4337 5332 0 0 3896 3968 129 131 92 94 90 93 10630 9669 .888 1.126 1.229 1.187 1.099 2.331 120 449 1.081 .92 120 2200 9540 64 76 129 141 0 7102 319 6783 1.357 6743 6424 .737 1.481 .44 .567
6 12045 14004 627 286 11418 13718 12356 14921 641 307 11729 14635 0 0 5724 6128 130 107 98 99 98 97 25136 26364 .832 1.201 1.248 1.227 1.172 1.999 120 424 1.182 .93 120 2350 9540 64 76 144 156 0 16872 345 16528 1.448 17977 17633 .691 1.503 .534 .588
7 9330 7821 621 295 8709 7526 8022 6925 631 313 7401 6630 0 0 5187 4015 127 114 100 100 100 100 16235 14031 1.157 .864 .896 .879 .863 1.59 80 348 .831 .9 110 2500 9540 64 75 159 170 0 9423 355 9067 1.041 8343 7988 .96 1.079 .058 .11
8 6834 7060 614 303 6220 6757 6993 6799 630 348 6379 6496 0 0 2758 3054 139 163 100 100 100 100 12977 12875 .921 1.086 1.018 1.118 1.01 1.78 80 304 1.09 .85 100 2640 9540 65 75 174 184 0 8506 365 8141 1.309 8192 7827 .764 1.227 .388 .295
9 11398 8650 619 280 10779 8370 12246 8643 636 293 11627 8363 0 0 4177 3056 120 103 100 100 100 100 19149 19990 1.288 .777 .719 .814 .74 1.53 80 386 .74 .92 110 2790 9540 64 75 188 199 0 10422 337 10084 .936 10413 10076 1.069 .867 -.096 -.207
10 6227 11373 621 281 5606 11092 5313 10637 639 295 4692 10356 0 0 3922 7942 135 90 98 100 96 100 16698 15048 .505 1.979 2.207 2.089 2.073 2.406 52 222 2.086 .93 80 2950 9550 67 75 206 214 0 13702 339 13364 2.384 12816 12477 .419 2.659 1.253 1.411
11 6789 9487 649 306 6140 9181 7016 9557 700 372 6367 9251 0 0 2281 4011 577 477 96 100 96 97 15321 15618 .669 1.495 1.453 1.499 1.461 1.744 80 332 1.69 .87 100 3080 9530 64 74 218 228 0 11430 369 11061 1.802 11514 11146 .555 1.751 .849 .808
12 8214 8759 641 325 7573 8434 8604 9405 672 356 7963 9080 0 0 4508 4021 231 194 95 100 92 100 16007 17043 .898 1.114 1.14 1.332 1.093 2.138 80 361 1.04 .91 110 3220 9540 64 75 231 242 0 10553 392 10161 1.342 11331 10940 .745 1.374 .424 .458
13 8833 10039 637 346 8196 9693 7971 9489 662 373 7334 9143 0 0 5484 6072 140 153 100 98 98 97 17889 16477 .846 1.183 1.247 1.26 1.131 2.023 80 324 1.166 .9 100 3370 9540 65 75 247 257 0 12095 417 11678 1.425 11433 11016 .702 1.502 .511 .587
14 5003 7076 625 331 4378 6745 4784 7152 639 361 4159 6821 0 0 2294 2980 122 135 98 100 98 100 11123 10980 .649 1.541 1.64 1.597 1.544 1.486 80 326 1.458 .9 110 3520 9540 64 75 261 272 0 8525 399 8127 1.856 8617 8218 .539 1.976 .892 .983
15 5299 6219 618 301 4681 5918 5768 6695 642 329 5150 6394 0 0 2738 3194 152 132 97 100 95 99 10599 11544 .791 1.264 1.242 1.393 1.276 1.935 120 392 1.254 .92 120 3670 9540 64 76 276 288 0 7493 363 7130 1.523 8066 7704 .657 1.496 .607 .581
16 6390 8135 615 290 5775 7845 4756 5130 647 317 4141 4840 0 0 5371 7928 180 140 93 96 91 95 13620 8981 .736 1.358 1.169 1.398 1.297 1.762 80 358 1.42 .95 110 3800 9530 63 74 289 300 0 9801 349 9452 1.637 6181 5831 .611 1.408 .711 .494
17 6553 10242 608 285 5945 9957 5875 9380 655 339 5267 9095 0 0 4124 6341 238 191 93 100 93 93 15902 14362 .597 1.675 1.727 1.615 1.655 2.027 32 140 1.584 .92 60 3950 9550 68 74 307 313 0 12340 343 11996 2.018 11301 10958 .496 2.08 1.013 1.057
18 9916 12459 635 309 9281 12150 10223 12466 656 325 9588 12157 0 0 5943 8205 135 113 96 98 96 98 21431 21745 .764 1.309 1.268 1.252 1.215 1.798 52 309 1.353 .96 90 4100 9530 64 73 320 329 0 15011 372 14639 1.577 15019 14647 .634 1.528 .657 .611
19 5187 11792 604 306 4583 11486 5387 11064 624 325 4783 10758 0 0 2787 7412 131 113 100 100 96 100 16069 15541 .399 2.506 2.249 2.717 2.357 1.655 32 214 2.543 .91 70 4240 9540 66 73 335 342 0 14207 369 13839 3.02 13330 12961 .331 2.71 1.594 1.438
20 7560 10096 614 321 6946 9775 6421 7295 683 414 5807 6974 0 0 4657 6715 295 344 100 100 96 100 16721 12781 .711 1.407 1.201 1.513 1.429 1.821 32 232 1.42 .87 70 4390 9530 65 72 350 357 0 12164 387 11777 1.696 8789 8402 .59 1.447 .762 .533

Total number of rows: 42624

Table truncated, full table size 9649 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap