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Sample GSM72951 Query DataSets for GSM72951
Status Public on Aug 31, 2005
Title C2
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 C2
Organism Mus musculus
Characteristics gastric biopsy JO11 C2
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29637.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 9782 11699 1829 2179 7953 9520 10110 12224 1872 2287 8281 10045 0 0 7729 9205 452 778 73 72 70 71 17473 18326 .835 1.197 1.213 1.224 1.213 1.391 80 417 1.216 .95 100 1670 8780 85 95 78 88 0 6802 1267 5535 .696 7107 5840 1.437 .705 -.523 -.504
2 13519 17351 1872 2200 11647 15151 9548 14801 1946 2362 7676 12601 0 0 9837 11662 508 927 86 91 85 87 26798 20277 .769 1.301 1.642 1.343 1.3 1.583 80 314 1.25 .97 100 1830 8790 86 96 94 104 0 10088 1279 8809 .756 8605 7326 1.322 .954 -.403 -.067
3 8529 10745 1728 2032 6801 8713 8307 11467 1807 2115 6579 9435 0 0 5438 6996 558 639 86 80 82 76 15514 16014 .781 1.281 1.434 1.131 1.312 1.831 80 421 1.286 .97 110 1960 8780 84 95 106 117 0 6247 1181 5066 .745 6667 5485 1.343 .834 -.425 -.262
4 9929 12771 1692 1834 8237 10937 10993 14376 1915 2236 9301 12542 0 0 3824 4429 957 1359 93 93 93 93 19174 21843 .753 1.328 1.348 1.336 1.332 1.212 32 203 1.294 .96 70 2110 8770 85 92 123 130 0 7425 1066 6359 .772 8358 7292 1.295 .784 -.373 -.351
5 6099 7501 1552 1640 4547 5861 6399 8280 1703 1861 4847 6640 0 0 3155 3945 703 1004 84 85 81 82 10408 11487 .776 1.289 1.37 1.271 1.264 1.569 120 516 1.291 .97 120 2260 8780 84 96 136 148 0 4361 953 3408 .749 4814 3860 1.334 .796 -.416 -.328
6 18346 21225 1582 1631 16764 19594 21802 23637 1805 1969 20220 22006 0 0 10172 11542 1432 2073 86 86 80 82 36358 42226 .856 1.169 1.088 1.21 1.156 1.691 120 469 1.161 .98 120 2410 8780 84 96 151 163 0 12340 948 11392 .68 13742 12794 1.472 .633 -.557 -.66
7 12854 16045 1676 1952 11178 14093 13646 18641 2190 2574 11970 16689 0 0 6212 7497 2195 2752 90 88 80 84 25271 28659 .793 1.261 1.394 1.292 1.234 1.342 52 263 1.271 .97 80 2550 8770 85 93 167 175 0 9328 1135 8194 .733 10838 9703 1.364 .811 -.448 -.303
8 10352 14342 1939 2409 8413 11933 10328 14303 2494 2818 8389 11894 0 0 5124 6123 2663 2007 81 96 75 90 20346 20283 .705 1.418 1.418 1.532 1.432 1.313 32 158 1.34 .95 60 2700 8770 86 92 183 189 0 8338 1401 6938 .825 8316 6915 1.213 .824 -.278 -.279
9 12407 17915 1817 2141 10590 15774 10709 14912 1946 2331 8892 12771 0 0 8465 12234 817 1107 90 90 85 85 26364 21663 .671 1.49 1.436 1.503 1.46 1.609 120 501 1.478 .98 120 2850 8780 84 96 195 207 0 10416 1245 9171 .866 8670 7425 1.155 .835 -.208 -.26
10 2524 2409 1769 2011 755 398 1783 1693 2024 2377 14 -318 0 0 2611 2819 1371 1706 12 9 9 3 1153 -304 1.897 .527 null 1.32 1.531 2.815 32 140 1.446 .93 60 2980 8760 85 91 211 217 0 1401 1169 231 .306 984 null 3.263 null -1.706 null
11 10072 13249 1781 2146 8291 11103 9337 12334 1970 2422 7556 10188 0 0 5245 6525 783 1231 92 92 92 92 19394 17744 .747 1.339 1.348 1.334 1.313 1.248 52 310 1.333 .96 80 3140 8770 85 93 226 234 0 7703 1248 6455 .779 7171 5923 1.284 .784 -.361 -.351
12 13723 18311 1712 2118 12011 16193 13660 17966 1921 2297 11948 15848 0 0 7062 8965 797 968 100 100 100 100 28204 27796 .742 1.348 1.326 1.387 1.358 1.324 32 226 1.362 .97 70 3290 8770 85 92 241 248 0 10646 1231 9415 .784 10445 9214 1.276 .771 -.351 -.375
13 16824 20765 1646 1967 15178 18798 17515 21332 1958 2362 15869 19365 0 0 8001 10003 1146 1400 100 96 100 96 33976 35234 .807 1.239 1.22 1.19 1.261 1.327 32 221 1.289 .96 70 3430 8770 85 92 255 262 0 12073 1144 10929 .72 12402 11259 1.389 .709 -.474 -.495
14 7164 8691 1662 1888 5502 6803 7470 9154 1871 2179 5808 7266 0 0 3165 3957 1026 1204 92 92 90 84 12305 13074 .809 1.236 1.251 1.2 1.198 1.176 52 300 1.253 .97 90 3580 8770 84 93 269 278 0 5053 1098 3955 .719 5322 4224 1.391 .727 -.476 -.459
15 8650 11528 1640 1870 7010 9658 7435 10295 1789 2116 5795 8425 0 0 5207 7672 849 1148 87 88 85 86 16668 14220 .726 1.378 1.454 1.355 1.399 1.368 80 470 1.428 .98 110 3720 8770 83 94 282 293 0 6702 1087 5615 .801 5985 4898 1.248 .845 -.32 -.243
16 5099 6690 1678 1878 3421 4812 4223 5331 1782 2047 2545 3453 0 0 3208 4476 619 892 96 90 87 84 8233 5998 .711 1.407 1.357 1.398 1.346 1.61 32 216 1.42 .97 70 3860 8760 84 91 298 305 0 3890 1092 2798 .818 3099 2008 1.223 .789 -.29 -.342
17 9800 14779 1396 1531 8404 13248 8159 12046 1702 2504 6763 10515 0 0 5709 9530 1636 4518 100 91 83 58 21652 17278 .634 1.576 1.555 1.562 1.624 1.185 12 68 1.401 .98 40 4000 8780 88 92 314 318 0 8592 890 7702 .917 7003 6113 1.091 .904 -.126 -.146
18 21984 34631 1681 2158 20303 32473 24489 36034 1860 2557 22808 33876 0 0 7581 11440 823 1476 100 100 100 100 52776 56684 .625 1.599 1.485 1.637 1.649 1.148 32 176 1.603 .98 60 4150 8770 86 92 328 334 0 20134 1255 18880 .93 20950 19695 1.075 .864 -.105 -.212
19 18957 29431 1517 1663 17440 27768 17140 27506 1617 1855 15623 25843 0 0 7086 12202 844 1261 100 100 100 100 45208 41466 .628 1.592 1.654 1.554 1.594 1.348 12 104 1.613 .95 50 4310 8770 86 91 344 349 0 17111 967 16144 .926 15992 15025 1.08 .962 -.111 -.056
20 7900 10383 1743 2075 6157 8308 6511 10153 1943 2461 4768 8078 0 0 3838 3103 1334 1704 100 100 91 100 14465 12846 .741 1.349 1.694 1.497 1.374 1.477 12 104 1.435 .92 50 4440 8770 86 91 357 362 0 6037 1206 4830 .785 5903 4697 1.275 .985 -.35 -.022

Total number of rows: 42624

Table truncated, full table size 9988 Kbytes.




Supplementary data files not provided
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