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Sample GSM72958 Query DataSets for GSM72958
Status Public on Aug 31, 2005
Title C7
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 C7
Organism Mus musculus
Characteristics gastric biopsy JO11 C7
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, Helicobacter pylori
Image: http://smd.stanford.edu/MicroArray/gifs/2002-06/29648.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 1618 4202 301 171 1317 4031 1638 3949 347 240 1337 3778 0 0 653 1891 309 347 96 98 85 95 5348 5115 .327 3.061 2.826 3.106 2.91 1.437 80 486 3.028 .92 110 1880 9070 37 48 94 105 0 1464 60 1405 1.066 1376 1316 .938 .985 .093 -.022
2 1664 3921 293 166 1371 3755 1570 3798 326 249 1277 3632 0 0 684 1263 168 390 100 100 98 100 5126 4909 .365 2.739 2.844 2.947 2.868 1.566 52 277 2.688 .92 90 2020 9080 39 48 109 118 0 1366 58 1308 .954 1323 1266 1.048 .991 -.067 -.013
3 1142 2650 280 154 862 2496 1046 2564 286 161 766 2410 0 0 304 931 56 69 100 100 100 98 3358 3176 .345 2.896 3.146 2.731 2.939 1.503 52 312 3.192 .93 90 2170 9080 39 48 124 133 0 923 54 870 1.009 893 840 .991 1.096 .013 .133
4 920 2228 281 157 639 2071 930 2221 283 167 649 2064 0 0 189 873 67 67 100 96 100 96 2710 2713 .309 3.241 3.18 2.749 3.159 2.36 52 276 4.217 .85 90 2310 9080 39 48 138 147 0 776 55 722 1.129 774 719 .886 1.108 .175 .148
5 919 2221 286 163 633 2058 909 2150 290 174 623 1987 0 0 404 1368 60 71 92 95 90 95 2691 2610 .308 3.251 3.189 2.984 3.131 1.899 120 493 3.575 .9 120 2460 9070 37 49 152 164 0 774 57 717 1.133 749 692 .883 1.111 .18 .152
6 1437 3616 287 167 1150 3449 1366 3473 289 178 1079 3306 0 0 504 1691 44 66 96 100 96 98 4599 4385 .333 2.999 3.064 2.821 2.946 1.649 80 381 3.172 .94 110 2600 9070 37 48 166 177 0 1260 58 1202 1.045 1210 1152 .957 1.068 .063 .094
7 973 2511 290 162 683 2349 923 2307 295 173 633 2145 0 0 418 1264 46 57 92 97 92 97 3032 2778 .291 3.439 3.389 3.369 3.341 1.714 80 376 3.51 .92 100 2750 9070 38 48 182 192 0 875 56 818 1.198 804 747 .834 1.181 .261 .24
8 904 2338 293 162 611 2176 925 2254 301 191 632 2092 0 0 408 1214 60 116 90 97 86 96 2787 2724 .281 3.561 3.31 3.816 3.46 1.739 80 338 3.621 .93 100 2900 9080 39 49 197 207 0 815 56 758 1.241 785 729 .806 1.153 .311 .206
9 1649 4587 293 172 1356 4415 1676 4679 308 220 1383 4507 0 0 458 1507 97 259 100 100 100 100 5771 5890 .307 3.256 3.259 3.263 3.374 1.391 52 291 3.314 .95 90 3040 9090 40 49 211 220 0 1598 60 1538 1.134 1630 1570 .881 1.135 .182 .183
10 1162 3568 305 172 857 3396 1009 3595 315 204 704 3423 0 0 749 2407 60 191 87 93 78 87 4253 4127 .252 3.963 4.862 4.458 4.339 1.854 32 213 3.816 .94 70 3210 9060 38 45 229 236 0 1243 60 1183 1.381 1253 1193 .724 1.694 .465 .761
11 986 2759 295 165 691 2594 1002 2838 309 218 707 2673 0 0 241 1022 97 338 100 100 98 100 3285 3380 .266 3.754 3.781 3.646 3.833 1.48 52 316 3.978 .92 90 3340 9090 40 49 241 250 0 961 57 904 1.308 989 931 .765 1.317 .387 .398
12 1026 2875 285 153 741 2722 1048 3070 289 185 763 2917 0 0 354 1300 67 177 94 94 94 94 3463 3680 .272 3.673 3.823 3.098 3.452 2.248 52 317 3.94 .9 90 3490 9080 39 48 256 265 0 1002 53 948 1.28 1070 1016 .781 1.332 .356 .414
13 1029 2984 285 153 744 2831 998 3018 296 206 713 2865 0 0 384 1354 95 295 92 100 90 98 3575 3578 .263 3.805 4.018 3.893 3.813 1.82 52 222 3.764 .93 80 3630 9090 41 49 271 279 0 1040 53 986 1.326 1052 998 .754 1.4 .407 .486
14 896 2788 291 155 605 2633 904 2499 295 165 613 2344 0 0 415 1626 47 62 90 100 88 96 3238 2957 .23 4.352 3.824 4.079 3.962 1.716 80 349 4.47 .92 100 3770 9070 38 48 284 294 0 971 54 917 1.516 871 817 .659 1.332 .601 .414
15 841 2188 296 152 545 2036 831 2195 303 165 535 2043 0 0 357 1147 55 64 88 96 86 95 2581 2578 .268 3.736 3.819 3.312 3.617 2.315 80 354 4.249 .9 100 3910 9080 39 49 298 308 0 762 53 709 1.302 765 712 .768 1.331 .38 .412
16 804 2341 294 152 510 2189 778 2293 304 192 484 2141 0 0 307 1408 66 190 94 94 94 94 2699 2625 .233 4.292 4.424 3.066 3.972 2.772 52 299 4.676 .88 90 4050 9080 39 48 312 321 0 816 53 763 1.496 799 746 .669 1.541 .581 .624
17 1121 3240 289 153 832 3087 1084 2969 312 240 795 2816 0 0 419 1884 129 475 100 100 100 91 3919 3611 .27 3.71 3.542 3.5 3.309 1.522 12 68 4.209 .92 40 4200 9070 41 45 330 334 0 1129 53 1076 1.293 1034 981 .774 1.234 .37 .304
18 1466 4492 290 157 1176 4335 1397 4297 291 164 1107 4140 0 0 523 2364 47 55 100 100 100 100 5511 5247 .271 3.686 3.74 3.471 3.507 1.475 32 164 3.929 .94 60 4360 9080 41 47 345 351 0 1565 55 1510 1.284 1497 1443 .779 1.303 .361 .382
19 1072 3233 295 151 777 3082 1130 3580 317 243 835 3429 0 0 286 1272 132 391 100 100 100 91 3859 4264 .252 3.967 4.107 3.789 3.814 1.579 12 104 3.862 .93 50 4490 9070 40 45 358 363 0 1126 53 1074 1.382 1247 1195 .724 1.431 .467 .517
20 1208 3988 290 150 918 3838 1156 4026 295 154 866 3876 0 0 457 1921 43 49 100 100 100 100 4756 4742 .239 4.181 4.476 4.16 4.418 1.478 32 232 4.263 .93 70 4650 9080 40 47 373 380 0 1390 52 1337 1.457 1403 1351 .686 1.559 .543 .641

Total number of rows: 42624

Table truncated, full table size 9306 Kbytes.




Supplementary data files not provided
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