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Sample GSM39910 Query DataSets for GSM39910
Status Public on Feb 21, 2005
Title Prostate 0782
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Prostate 0782
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2001-10/20947.gif
 
Submission date Jan 26, 2005
Last update date Nov 22, 2005
Contact name Jonathan Pollack
E-mail(s) pollack1@stanford.edu
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
1 393 349 123 82 270 267 409 317 127 86 286 235 0 0 141 158 77 41 88 94 78 86 537 521 1.011 .989 .822 .864 .963 2.755 52 376 .908 .74 90 1320 7650 56 65 51 60 0 162 38 124 .46 147 109 2.174 .382 -1.12 -1.388 -1.12
2 329 167 129 81 200 86 342 164 129 87 213 83 0 0 117 66 72 48 83 66 73 43 286 296 2.326 .43 .39 .393 .423 2.645 80 387 .295 .6 100 1470 7650 56 66 66 76 0 78 38 40 .2 76 39 5 .181 -2.322 -2.464 -2.322
3 731 961 119 85 612 876 837 856 142 118 718 771 0 0 382 523 246 166 75 96 68 84 1488 1489 .699 1.431 1.074 1.519 1.489 3.689 32 200 1.209 .75 70 1620 7640 56 63 82 89 -100 447 40 407 .666 398 359 1.502 .499 -1.002 -.587
4 577 3668 108 98 469 3570 236 1093 187 501 128 995 0 0 716 5681 376 3163 34 28 25 18 4039 1123 .131 7.612 7.773 2.203 2.566 5.733 32 150 10.425 .57 60 1740 7640 57 63 95 101 -100 1706 46 1660 3.54 508 463 .282 3.616 1.854 1.824
5 139 127 145 97 -6 30 66 62 157 228 -79 -35 0 0 176 168 156 1836 15 0 5 0 24 -114 null null null .562 .547 2.048 80 447 21.989 .42 100 1900 7650 56 66 109 119 -50 59 45 14 null 29 null null null null null
6 451 327 126 85 325 242 456 371 136 102 330 286 0 0 67 156 95 66 100 83 100 75 567 616 1.343 .745 .867 .92 .949 1.673 12 104 .784 .65 50 2040 7660 59 64 125 130 0 152 40 113 .346 173 133 2.887 .403 -1.53 -1.311 -1.53
7 524 395 138 93 386 302 581 400 143 107 443 307 0 0 182 118 84 65 90 96 84 88 688 750 1.278 .782 .693 .766 .755 1.7 52 305 .669 .79 90 2190 7660 57 66 138 147 0 184 43 140 .364 186 143 2.748 .322 -1.458 -1.633 -1.458
8 3007 9075 134 95 2873 8980 3119 9088 136 105 2985 8993 0 0 1640 5673 73 57 96 100 91 96 11853 11978 .32 3.126 3.013 3.017 3.284 2.582 80 429 3.42 .93 110 2340 7650 55 66 152 163 0 4221 44 4177 1.454 4227 4183 .688 1.401 .54 .487 .54
9 650 1059 143 102 507 957 694 1149 145 109 551 1047 0 0 204 330 38 42 90 100 90 100 1464 1598 .53 1.888 1.9 1.74 1.825 2.1 32 216 2.097 .82 70 2480 7650 57 64 168 175 0 493 47 445 .878 534 487 1.139 .884 -.188 -.178 -.188
10 384 439 153 104 231 335 404 467 154 108 251 363 0 0 120 123 34 39 93 96 90 90 566 614 .69 1.45 1.446 1.23 1.27 2.05 32 218 1.396 .72 70 2630 7660 58 65 183 190 0 204 48 156 .675 217 169 1.483 .673 -.568 -.572 -.568
11 781 1493 150 111 631 1382 812 1477 156 116 662 1366 0 0 365 806 38 37 96 100 96 98 2013 2028 .457 2.19 2.063 2.083 2.162 1.844 52 253 2.323 .93 80 2780 7660 58 66 198 206 0 694 52 643 1.019 687 635 .982 .96 .027 -.059 .027
12 879 1374 150 113 729 1261 940 1481 153 119 790 1368 0 0 305 409 38 42 94 100 94 100 1990 2158 .578 1.73 1.732 1.787 1.611 1.964 52 312 1.725 .89 90 2910 7650 56 65 210 219 0 639 53 587 .805 689 636 1.243 .805 -.314 -.312 -.314
13 541 929 146 116 395 813 582 910 150 121 436 794 0 0 192 344 39 43 94 100 90 100 1208 1230 .486 2.058 1.821 2.014 2.121 1.847 52 312 2.2 .85 90 3070 7660 57 66 226 235 0 432 54 378 .957 423 369 1.045 .847 -.063 -.24 -.063
14 378 382 160 121 218 261 382 392 161 125 222 271 0 0 115 119 41 39 94 98 94 88 479 493 .835 1.197 1.221 1.085 1.293 1.8 52 246 1.192 .75 80 3210 7650 57 65 241 249 0 178 56 121 .557 182 126 1.796 .568 -.845 -.817 -.845
15 3305 9062 156 121 3149 8941 3496 9984 159 126 3340 9863 0 0 1660 4679 41 43 97 100 97 100 12090 13203 .352 2.839 2.953 2.555 2.768 1.855 80 369 2.972 .94 100 3360 7650 56 66 255 265 0 4215 56 4159 1.321 4644 4587 .757 1.373 .401 .458 .401
16 1246 5793 152 126 1094 5667 1300 6383 156 127 1148 6257 0 0 363 1701 40 41 94 100 94 100 6761 7405 .193 5.18 5.45 4.969 5.271 1.427 52 300 5.441 .92 90 3500 7650 56 65 269 278 0 2694 59 2636 2.409 2969 2910 .415 2.535 1.269 1.342 1.269
17 292 360 155 119 137 241 293 361 156 123 138 242 0 0 90 103 37 38 90 98 80 94 378 380 .568 1.759 1.754 1.718 1.505 1.874 52 266 1.703 .7 80 3650 7660 58 66 285 293 0 167 55 112 .818 168 113 1.222 .816 -.289 -.294 -.289
18 338 269 165 119 173 150 337 279 166 123 172 160 0 0 139 82 38 38 84 90 75 84 323 332 1.153 .867 .93 .766 .751 1.924 32 158 .63 .61 60 3790 7660 59 65 300 306 0 125 55 70 .403 130 74 2.48 .433 -1.31 -1.209 -1.31
19 632 1525 158 132 474 1393 567 1471 163 135 409 1339 0 0 314 882 41 41 94 100 90 98 1867 1748 .34 2.939 3.274 2.68 2.9 2.032 52 297 3.188 .9 80 3940 7660 58 66 314 322 0 709 61 648 1.367 684 623 .732 1.523 .451 .607 .451
20 376 330 162 117 214 213 418 337 163 126 256 220 0 0 114 91 37 39 90 93 87 90 427 476 1.005 .995 .859 .847 .83 1.99 32 199 1.008 .74 70 4090 7650 57 64 329 336 0 153 54 99 .463 157 102 2.16 .4 -1.111 -1.323 -1.111

Total number of rows: 43008

Table truncated, full table size 9372 Kbytes.




Supplementary data files not provided

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