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Sample GSM88661 Query DataSets for GSM88661
Status Public on Dec 21, 2005
Title REH t(12;21) 2
Sample type RNA
 
Channel 1
Source name Common Reference F
Organism Homo sapiens
Characteristics Common Reference F
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name REH t(12;21)
Organism Homo sapiens
Characteristics REH t(12;21)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: acute lymphoblastic leukemia, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14242.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Dec 20, 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 GPL3266
Series (2)
GSE3883 ALL Cell Lines
GSE4384 Gene expression patterns associated with recurrent chromosomal translocations in acute lymphoblastic leukemia

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 968 745 297 384 671 361 955 736 297 392 658 352 0 0 168 164 66 101 100 96 100 90 1032 1010 1.859 .538 .535 .545 .528 .205 32 131 .464 .71 60 1510 8040 85 91 48 54 0 1025 528 496 .74 1012 484 1.352 .736 -.435 -.443
2 2483 7225 270 368 2213 6857 2462 7199 276 376 2192 6831 0 0 1143 3379 62 114 100 100 100 100 9070 9023 .323 3.099 3.116 3.6 3.055 1.773 32 156 2.719 .89 60 1650 8030 84 90 62 68 0 9936 506 9430 4.261 9900 9394 .235 4.286 2.091 2.099
3 6971 3022 253 265 6718 2757 6213 2920 261 274 5960 2655 0 0 3065 1313 66 112 100 100 100 100 9475 8615 2.437 .41 .445 .432 .442 .182 52 275 .379 .89 90 1780 8010 80 89 73 82 0 4156 364 3791 .564 4016 3651 1.772 .613 -.825 -.707
4 545 460 267 251 278 209 294 250 269 257 27 -1 0 0 649 548 57 91 40 26 27 18 487 26 1.33 .752 null 2.265 .881 6.931 80 291 .742 .87 100 1930 8020 81 91 88 98 -50 633 345 287 1.034 344 -1 .967 null .048 null
5 2410 909 268 265 2142 644 2572 871 270 272 2304 606 0 0 736 354 55 88 100 93 98 90 2786 2910 3.326 .301 .263 .324 .294 .237 80 281 .286 .88 100 2050 8020 81 91 100 110 0 1250 364 886 .413 1198 833 2.419 .362 -1.274 -1.467
6 345 396 236 222 109 174 262 314 242 235 26 92 0 0 245 307 52 104 36 45 22 17 283 118 .626 1.596 3.538 3.262 1.442 7.401 80 312 .974 .72 100 2210 8020 81 91 116 126 -50 545 305 239 2.195 432 127 .456 4.866 1.134 2.283
7 2806 1746 247 243 2559 1503 2854 1830 247 251 2607 1587 0 0 471 434 52 109 100 100 100 100 4062 4194 1.703 .587 .609 .6 .627 .184 52 224 .555 .91 90 2330 8020 81 90 128 137 0 2401 334 2067 .808 2517 2182 1.238 .837 -.308 -.256
8 1257 672 238 197 1019 475 1269 653 258 240 1031 456 0 0 327 230 182 312 100 75 100 25 1494 1487 2.145 .466 .442 .467 .454 .193 52 228 .428 .84 80 2460 8020 82 90 142 150 0 924 271 653 .641 898 627 1.56 .608 -.642 -.717
9 2005 930 239 173 1766 757 2065 946 267 224 1826 773 0 0 885 450 206 353 100 78 96 56 2523 2599 2.333 .429 .423 .535 .548 .347 32 174 .301 .49 70 2610 8010 81 88 157 164 0 1279 238 1041 .589 1301 1063 1.696 .582 -.762 -.781
10 703 595 221 167 482 428 687 600 222 171 466 433 0 0 168 216 57 54 100 96 100 94 910 899 1.126 .888 .929 .935 .904 .539 52 240 .811 .85 90 2730 8020 81 90 168 177 0 818 230 589 1.221 825 595 .819 1.278 .288 .354
11 4795 7664 201 157 4594 7507 5240 8561 209 170 5039 8404 0 0 1539 3240 60 88 100 100 100 100 12101 13443 .612 1.634 1.668 1.642 1.723 .6 80 316 1.631 .95 100 2870 8030 82 92 182 192 0 10539 216 10324 2.247 11773 11557 .445 2.294 1.168 1.198
12 1598 1835 205 160 1393 1675 1616 1826 220 181 1411 1666 0 0 627 653 75 98 100 100 100 100 3068 3077 .832 1.202 1.181 1.381 1.175 .717 32 187 1.007 .88 70 3000 8010 81 88 196 203 0 2523 220 2303 1.654 2511 2291 .605 1.624 .726 .699
13 1222 1606 216 156 1006 1450 1178 1502 224 167 962 1346 0 0 330 560 56 62 100 100 100 100 2456 2308 .694 1.441 1.399 1.483 1.425 .436 52 307 1.213 .87 90 3150 8020 81 90 210 219 0 2209 215 1994 1.982 2066 1851 .505 1.924 .987 .944
14 1552 1314 226 167 1326 1147 1465 1241 231 171 1239 1074 0 0 518 445 52 54 100 100 100 100 2473 2313 1.156 .865 .867 .962 .941 .477 52 294 .731 .84 90 3290 8010 80 89 224 233 0 1807 230 1577 1.19 1707 1477 .841 1.192 .25 .253
15 1086 1144 225 157 861 987 979 1080 229 163 754 923 0 0 369 485 55 60 100 100 100 96 1848 1677 .872 1.146 1.224 1.225 1.182 .551 52 246 1.075 .88 90 3440 7990 78 87 239 248 0 1573 216 1357 1.576 1485 1269 .634 1.683 .657 .751
16 3196 1519 232 164 2964 1355 3422 1628 236 168 3190 1464 0 0 879 573 56 56 100 98 100 96 4319 4654 2.187 .457 .459 .456 .478 .157 80 299 .456 .94 100 3560 8020 81 91 251 261 0 2089 226 1863 .629 2239 2013 1.591 .631 -.67 -.664
17 2366 2630 230 183 2136 2447 2293 2437 255 197 2063 2254 0 0 661 651 171 129 100 100 100 100 4583 4317 .873 1.146 1.093 1.188 1.107 .259 52 239 1.051 .95 90 3700 8030 82 91 265 274 0 3617 252 3365 1.575 3351 3100 .635 1.503 .656 .587
18 1806 1189 226 169 1580 1020 1797 1112 250 187 1571 943 0 0 480 414 170 130 100 98 100 96 2600 2514 1.549 .646 .6 .656 .633 .255 52 242 .606 .9 90 3840 8030 82 91 279 288 0 1635 232 1403 .888 1529 1297 1.126 .825 -.172 -.277
19 1076 1086 210 154 866 932 991 1042 216 159 781 888 0 0 365 405 47 50 100 100 100 100 1798 1669 .929 1.076 1.137 1.136 1.04 .471 52 221 .972 .91 80 3970 8030 83 91 293 301 0 1493 212 1282 1.48 1433 1221 .676 1.564 .566 .645
20 3128 2143 204 152 2924 1991 3236 2216 208 158 3032 2064 0 0 1283 1088 47 51 100 100 100 97 4915 5096 1.469 .681 .681 .698 .737 .357 80 314 .66 .92 100 4120 8030 82 92 307 317 0 2947 209 2738 .936 3047 2838 1.068 .936 -.095 -.095

Total number of rows: 43392

Table truncated, full table size 9885 Kbytes.




Supplementary data files not provided
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