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Sample GSM72953 Query DataSets for GSM72953
Status Public on Aug 31, 2005
Title D6
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 D6
Organism Mus musculus
Characteristics gastric biopsy JO11 D6
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29646.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) 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 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 10828 22491 365 234 10463 22257 12498 23682 417 325 12133 23448 0 0 4521 10987 421 652 97 95 95 93 32720 35581 .47 2.127 1.933 1.956 1.844 2.548 80 448 2.449 .86 110 1660 9350 45 56 75 86 0 22050 229 21821 2.086 23218 22988 .48 1.895 1.06 .922
2 11953 13764 367 241 11586 13523 13599 15290 472 428 13232 15049 0 0 5996 6278 576 892 94 92 92 90 25109 28281 .857 1.167 1.137 1.245 1.063 2 52 270 1.173 .84 90 1800 9340 45 54 90 99 0 13494 236 13258 1.144 14990 14754 .874 1.115 .194 .157
3 8039 17114 364 233 7675 16881 8969 18647 406 287 8605 18414 0 0 3517 8590 317 348 97 98 96 98 24556 27019 .455 2.199 2.14 2.177 2.179 1.865 80 410 2.441 .88 110 1950 9350 45 56 104 115 0 16778 228 16550 2.156 18281 18053 .464 2.098 1.109 1.069
4 8111 14626 360 233 7751 14393 9053 14616 369 247 8693 14383 0 0 4120 7609 69 157 100 100 100 100 22144 23076 .539 1.857 1.655 1.98 1.697 2.318 80 406 2.098 .79 110 2090 9350 45 56 118 129 0 14339 228 14111 1.821 14329 14101 .549 1.622 .864 .698
5 9535 17460 366 227 9169 17233 10696 18059 647 683 10330 17832 0 0 4354 7675 2023 3015 88 88 83 87 26402 28162 .532 1.879 1.726 1.982 1.62 1.949 80 434 2.058 .84 110 2240 9350 45 56 133 144 0 17118 223 16895 1.843 17705 17482 .543 1.692 .882 .759
6 11303 28565 367 223 10936 28342 14395 30312 528 928 14028 30089 0 0 6052 13155 934 3853 94 96 84 86 39278 44117 .386 2.592 2.145 3.005 2.194 2.004 52 296 2.748 .84 90 2370 9350 46 55 147 156 0 28005 219 27786 2.541 29718 29499 .394 2.103 1.345 1.072
7 8697 12820 368 234 8329 12586 9320 14074 478 520 8952 13840 0 0 4418 6429 793 2255 88 92 86 82 20915 22792 .662 1.511 1.546 1.712 1.627 2.432 80 386 1.486 .88 100 2530 9360 47 57 163 173 0 12569 229 12339 1.481 13798 13569 .675 1.516 .567 .6
8 9680 13539 373 242 9307 13297 11196 14505 382 247 10823 14263 0 0 4472 6181 74 69 96 100 96 98 22604 25086 .7 1.429 1.318 1.517 1.303 2.321 80 304 1.487 .86 100 2680 9360 47 57 178 188 0 13274 237 13036 1.401 14221 13983 .714 1.292 .486 .37
9 8333 11989 378 248 7955 11741 8774 11610 386 250 8396 11362 0 0 5149 7511 76 61 96 100 95 98 19696 19758 .678 1.476 1.353 1.651 1.376 2.723 80 324 1.555 .87 100 2820 9360 47 57 192 202 0 11754 243 11511 1.447 11382 11139 .691 1.327 .533 .408
10 7224 7097 374 239 6850 6858 6881 5668 383 241 6507 5429 0 0 4843 5580 83 54 100 96 100 93 13708 11936 .999 1.001 .834 .882 .991 4.188 32 192 1.099 .83 70 2970 9370 49 56 208 215 0 6958 234 6724 .982 5557 5323 1.019 .818 -.027 -.29
11 7614 10698 383 254 7231 10444 8325 10554 445 378 7942 10300 0 0 4053 6294 338 926 91 96 86 91 17675 18242 .692 1.444 1.297 1.633 1.352 2.696 80 450 1.593 .86 110 3120 9360 46 57 221 232 0 10488 249 10239 1.416 10347 10098 .706 1.271 .502 .347
12 9027 9598 390 258 8637 9340 9871 9562 402 329 9481 9304 0 0 5325 4823 127 436 94 96 88 96 17977 18785 .925 1.081 .981 1.392 .978 3.135 52 296 .988 .93 90 3250 9350 46 55 235 244 0 9410 253 9157 1.06 9375 9122 .943 .962 .084 -.056
13 9342 13422 389 255 8953 13167 10948 14907 395 280 10559 14652 0 0 5679 7756 74 121 92 96 90 94 22120 25211 .68 1.471 1.388 1.91 1.315 3.425 52 289 1.449 .86 90 3400 9360 47 56 250 259 0 13159 250 12909 1.442 14615 14365 .694 1.36 .528 .444
14 5794 9243 389 280 5405 8963 5867 8520 393 287 5478 8240 0 0 3765 5350 73 97 96 100 93 100 14368 13718 .603 1.658 1.504 2.086 1.607 2.715 80 326 1.634 .88 100 3550 9350 46 56 265 275 0 9062 275 8787 1.626 8353 8078 .615 1.475 .701 .56
15 4061 7176 395 265 3666 6911 3750 7025 408 279 3355 6760 0 0 2748 3940 99 112 93 100 91 98 10577 10115 .53 1.885 2.015 2.204 1.839 2.696 80 323 1.633 .85 100 3690 9360 47 57 279 289 0 7035 260 6775 1.848 6887 6627 .541 1.975 .886 .982
16 9240 12008 399 257 8841 11751 9233 11329 408 268 8834 11072 0 0 7143 8132 94 92 93 98 92 98 20592 19906 .752 1.329 1.253 1.605 1.294 3.264 80 342 1.275 .89 100 3840 9360 47 57 294 304 0 11773 252 11521 1.303 11107 10855 .767 1.229 .382 .297
17 5731 5937 377 229 5354 5708 6196 4085 391 244 5819 3856 0 0 4820 5071 80 74 93 93 87 90 11062 9675 .938 1.066 .663 1.456 1.208 3.738 32 147 1.068 .86 60 3970 9360 49 55 309 315 0 5821 225 5596 1.045 4005 3780 .957 .65 .064 -.622
18 5032 9058 401 241 4631 8817 3523 9261 418 259 3122 9020 0 0 4258 6373 123 95 98 100 90 98 13448 12142 .525 1.904 2.889 2.225 1.727 4.507 52 247 1.938 .78 80 4130 9370 49 57 324 332 0 8880 236 8644 1.867 9079 8843 .536 2.833 .9 1.502
19 3079 7539 391 251 2688 7288 1426 4853 405 264 1035 4602 0 0 3257 7545 83 74 82 100 76 98 9976 5637 .369 2.711 4.446 3.164 2.249 4.803 52 253 3.277 .69 80 4270 9370 49 57 338 346 0 7391 246 7145 2.658 4758 4512 .376 4.359 1.41 2.124
20 5674 9754 387 258 5287 9496 4335 8620 399 270 3948 8362 0 0 4931 8685 85 82 96 98 94 94 14783 12310 .557 1.796 2.118 1.437 1.251 4.591 52 313 2.313 .64 90 4420 9360 47 56 352 361 0 9563 253 9310 1.761 8451 8198 .568 2.077 .816 1.054

Total number of rows: 42624

Table truncated, full table size 9522 Kbytes.




Supplementary data files not provided

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