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Sample GSM39911 Query DataSets for GSM39911
Status Public on Feb 21, 2005
Title Prostate 0805
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Prostate 0805
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-10/20948.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) [email protected]
Phone 650-736-1987
Organization name Stanford University
Department Pathology
Lab Pollack Lab
Street address 269 Campus Drive, CCSR3245A
City Stanford
State/province CA
ZIP/Postal code 94305-5176
Country USA
 
Platform ID GPL1823
Series (1)
GSE2193 Normal_human_tissues

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
VALUE same as UNF_VALUE but with flagged values removed
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
UNF_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

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 UNF_VALUE
1 387 472 154 132 233 340 409 495 161 137 255 363 0 0 136 168 66 55 90 98 75 88 573 618 .685 1.459 1.424 1.483 1.417 1.892 52 280 1.376 .78 80 1300 7730 33 41 50 58 0 251 70 181 .776 263 193 1.288 .757 -.366 -.401 -.366
2 331 314 155 136 176 178 328 314 161 143 173 178 0 0 103 91 67 56 90 96 67 78 354 351 .989 1.011 1.029 .932 .903 1.775 52 266 .989 .67 80 1450 7730 33 41 65 73 0 167 72 95 .538 167 95 1.859 .547 -.894 -.87 -.894
3 1084 1437 164 142 920 1295 1177 1635 169 148 1013 1493 0 0 442 542 44 43 96 100 94 100 2215 2506 .71 1.408 1.474 1.458 1.41 1.465 52 302 1.4 .95 90 1600 7740 33 42 79 88 0 764 76 689 .749 870 794 1.336 .784 -.417 -.351 -.417
4 1898 8510 176 151 1722 8359 928 4623 176 154 752 4472 0 0 1850 8234 47 44 96 100 90 100 10081 5224 .206 4.854 5.947 6.12 4.911 1.915 52 274 4.726 .97 80 1740 7730 33 41 94 102 0 4527 80 4446 2.582 2459 2379 .387 3.163 1.369 1.661 1.369
5 422 735 167 149 255 586 435 757 169 152 268 608 0 0 194 364 44 47 84 92 73 88 841 876 .435 2.298 2.269 2.367 2.104 1.772 52 312 2.192 .9 90 1890 7730 32 41 108 117 0 391 79 312 1.222 403 323 .818 1.207 .29 .271 .29
6 357 414 166 150 191 264 354 407 168 153 188 257 0 0 126 148 42 44 82 96 75 90 455 445 .723 1.382 1.367 1.35 1.306 2.612 52 332 1.328 .79 90 2030 7730 32 41 122 131 0 220 80 140 .735 216 137 1.36 .727 -.444 -.46 -.444
7 721 1596 162 151 559 1445 779 1677 164 155 617 1526 0 0 245 517 42 55 94 100 92 98 2004 2143 .387 2.585 2.473 2.568 2.605 1.402 52 284 2.586 .93 90 2180 7730 32 41 137 146 0 849 80 769 1.375 892 812 .727 1.316 .459 .396 .459
8 3056 11676 159 142 2897 11534 2922 12908 162 148 2763 12766 0 0 2336 8037 40 50 90 97 83 97 14431 15529 .251 3.981 4.62 4.58 3.906 1.597 80 378 3.84 .96 100 2320 7730 32 42 151 161 0 6211 76 6135 2.118 6866 6790 .472 2.458 1.083 1.297 1.083
9 600 1029 164 146 436 883 592 989 164 148 428 843 0 0 215 348 39 41 100 100 98 98 1319 1271 .494 2.025 1.97 2.096 2.034 1.49 52 266 1.957 .94 80 2470 7730 33 41 167 175 0 547 78 470 1.077 526 448 .928 1.048 .107 .067 .107
10 373 546 165 149 208 397 385 556 165 154 220 407 0 0 114 168 38 49 93 93 84 90 605 627 .524 1.909 1.85 1.889 1.638 1.847 32 220 1.955 .8 70 2620 7730 33 40 182 189 0 290 79 211 1.015 296 216 .985 .984 .022 -.023 .022
11 873 1451 159 151 714 1300 834 1405 161 156 675 1254 0 0 454 732 42 50 100 100 100 96 2014 1929 .549 1.821 1.858 1.813 1.823 1.606 52 318 1.805 .94 90 2770 7740 33 42 196 205 0 772 80 691 .968 747 667 1.033 .988 -.046 -.017 -.046
12 1152 1920 154 154 998 1766 1252 2056 161 157 1098 1902 0 0 410 621 38 46 96 100 96 100 2764 3000 .565 1.77 1.732 1.874 1.745 1.739 52 301 1.756 .95 90 2900 7730 32 41 209 218 0 1021 82 939 .941 1094 1012 1.062 .921 -.087 -.118 -.087
13 576 979 160 159 416 820 592 1054 165 162 432 895 0 0 224 386 40 47 92 96 92 96 1236 1327 .507 1.971 2.072 1.927 1.806 1.613 52 266 2.018 .9 80 3050 7730 33 41 225 233 0 521 85 436 1.048 561 476 .954 1.102 .068 .14 .068
14 383 452 160 156 223 296 393 434 164 162 233 278 0 0 133 199 40 48 90 86 84 82 519 511 .753 1.327 1.193 1.326 1.273 2.132 52 244 1.478 .83 80 3200 7730 33 41 240 248 0 240 83 157 .706 231 148 1.416 .635 -.502 -.656 -.502
15 4453 11774 163 152 4290 11622 5162 13491 168 161 4999 13339 0 0 2677 6917 56 52 98 100 95 100 15912 18338 .369 2.709 2.668 3.089 2.645 2.018 80 366 2.707 .98 100 3340 7730 32 42 253 263 0 6263 81 6182 1.441 7176 7095 .694 1.419 .527 .505 .527
16 1669 7801 155 148 1514 7653 1763 8230 159 167 1608 8082 0 0 488 2144 37 90 98 100 98 100 9167 9690 .198 5.055 5.026 5.15 5.177 1.276 52 246 5.156 .95 80 3490 7730 33 41 269 277 0 4149 79 4071 2.689 4378 4299 .372 2.673 1.427 1.419 1.427
17 315 450 160 168 155 282 317 450 159 183 157 282 0 0 87 134 37 92 92 94 86 78 437 439 .55 1.819 1.796 1.837 1.756 2.047 52 268 2.09 .69 80 3640 7730 33 41 284 292 0 239 89 150 .968 239 150 1.033 .955 -.047 -.066 -.047
18 340 399 160 182 180 217 361 408 160 187 201 226 0 0 101 95 42 55 83 100 75 83 397 427 .829 1.206 1.124 1.411 1.249 2.698 12 104 1.109 .61 50 3780 7730 34 39 299 304 0 212 97 115 .641 217 120 1.559 .598 -.641 -.742 -.641
19 671 1534 161 152 510 1382 699 1446 162 161 538 1294 0 0 308 932 40 47 96 98 92 94 1892 1832 .369 2.71 2.405 2.537 2.64 1.809 52 302 2.943 .92 80 3930 7730 33 41 313 321 0 816 81 735 1.441 769 688 .694 1.279 .527 .355 .527
20 337 378 157 170 180 208 349 373 162 174 192 203 0 0 107 132 41 50 84 82 80 76 388 395 .865 1.156 1.057 1.112 1.151 2.013 52 276 1.311 .71 80 4080 7740 34 42 328 336 0 201 90 111 .615 198 108 1.627 .562 -.702 -.83 -.702

Total number of rows: 43008

Table truncated, full table size 9370 Kbytes.




Supplementary data files not provided
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