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Sample GSM39942 Query DataSets for GSM39942
Status Public on Feb 21, 2005
Title Thymus 0512
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Thymus 0512
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-09/32613.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 GPL1824
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
1 594 735 246 264 348 471 496 532 277 292 250 268 0 0 470 974 209 155 55 66 34 45 819 518 .739 1.353 1.072 1.132 .774 4.107 120 660 2.522 .48 130 1590 8180 39 52 28 41 0 514 185 329 .946 372 187 1.057 .75 -.079 -.416 -.079
2 561 408 253 236 308 172 572 362 256 242 319 126 0 0 152 177 51 68 90 61 86 48 480 445 1.791 .558 .395 .489 .528 3.923 52 219 .306 .16 80 1740 8160 40 48 46 54 0 285 165 120 .391 253 88 2.561 .276 -1.357 -1.856 -1.357
3 1567 1617 250 247 1317 1370 1434 1310 292 279 1184 1063 0 0 912 1094 196 151 100 100 98 100 2687 2247 .961 1.04 .898 1.003 .918 1.529 52 316 1.05 .87 90 1870 8160 39 48 58 67 0 1131 173 958 .727 916 743 1.375 .628 -.459 -.672 -.459
4 5159 6725 255 240 4904 6485 5131 6260 295 265 4876 6020 0 0 2074 3116 194 138 98 100 98 100 11389 10896 .756 1.322 1.235 1.372 1.301 1.62 52 314 1.395 .94 90 2020 8160 39 48 73 82 0 4703 168 4535 .925 4378 4210 1.081 .863 -.113 -.212 -.113
5 689 1219 246 232 443 987 704 1206 251 236 458 974 0 0 173 269 52 74 98 100 98 100 1430 1432 .449 2.228 2.127 2.42 2.377 1.733 52 267 2.249 .87 80 2170 8160 40 48 89 97 0 852 162 690 1.558 843 681 .642 1.487 .64 .573 .64
6 622 759 240 226 382 533 639 746 245 227 399 520 0 0 125 145 53 64 100 100 96 98 915 919 .717 1.395 1.303 1.431 1.302 1.851 52 243 1.494 .79 80 2320 8160 40 48 104 112 0 531 158 373 .976 522 364 1.025 .911 -.035 -.134 -.035
7 791 4268 240 236 551 4032 826 4815 246 244 586 4579 0 0 269 1280 54 74 95 100 91 100 4583 5165 .137 7.318 7.814 8.416 7.575 1.81 80 355 7.281 .91 100 2460 8160 39 49 117 127 0 2985 165 2820 5.117 3367 3202 .195 5.464 2.355 2.45 2.355
8 6341 14317 241 243 6100 14074 7647 15705 246 253 7406 15462 0 0 3408 6488 52 74 97 100 97 100 20174 22868 .433 2.307 2.088 2.792 2.28 1.922 80 396 2.213 .95 100 2610 8160 39 49 132 142 0 10012 170 9842 1.613 10983 10813 .62 1.46 .69 .546 .69
9 587 927 247 255 340 672 574 935 245 261 327 680 0 0 231 160 51 77 84 100 81 100 1012 1007 .506 1.976 2.08 2.025 1.766 2.18 32 215 2.109 .61 70 2760 8160 40 47 148 155 0 648 178 470 1.382 654 476 .724 1.454 .467 .54 .467
10 312 345 237 216 75 129 296 287 242 229 59 71 0 0 96 205 50 73 55 48 30 30 204 130 .581 1.72 1.203 2.072 2.36 5.011 52 267 22.141 .05 80 2910 8150 39 47 163 171 -50 241 151 90 1.203 201 50 .831 .842 -.249 .266
11 1452 2379 238 223 1214 2156 1592 2522 242 236 1354 2299 0 0 435 636 50 77 100 100 100 100 3370 3653 .563 1.776 1.698 1.813 1.763 1.427 80 389 1.801 .94 100 3060 8150 38 48 177 187 0 1664 156 1508 1.242 1764 1608 .805 1.187 .313 .248 .313
12 841 1347 245 235 596 1112 977 1322 252 246 732 1087 0 0 408 384 55 82 84 100 84 100 1708 1819 .536 1.866 1.485 2.313 1.758 2.482 32 199 1.691 .88 70 3200 8150 39 46 192 199 0 942 164 778 1.305 924 760 .766 1.038 .384 .054 .384
13 764 1024 250 204 514 820 818 1081 251 209 568 877 0 0 286 256 53 73 90 100 90 100 1334 1445 .627 1.595 1.544 1.654 1.436 2.009 52 317 1.564 .83 90 3340 8150 38 47 205 214 0 716 143 573 1.116 756 613 .896 1.08 .158 .111 .158
14 872 947 254 177 618 770 591 657 264 185 337 480 0 0 1530 1277 73 69 84 100 84 100 1388 817 .803 1.246 1.424 1.36 1.353 1.979 32 206 .309 .74 70 3490 8150 39 46 221 228 0 662 124 538 .871 459 336 1.148 .996 -.199 -.006 -.199
15 4016 4852 251 187 3765 4665 4708 5035 271 206 4457 4848 0 0 2374 2589 154 130 90 96 86 96 8430 9305 .807 1.239 1.088 1.531 1.241 2.274 80 394 1.201 .95 100 3640 8150 38 48 235 245 0 3393 131 3262 .866 3521 3390 1.154 .761 -.207 -.395 -.207
16 1645 1969 241 226 1404 1743 1801 2017 256 240 1560 1791 0 0 677 537 92 94 96 100 94 100 3147 3351 .806 1.241 1.148 1.388 1.231 1.902 52 255 1.078 .88 80 3770 8150 39 47 249 257 0 1377 158 1219 .868 1410 1252 1.152 .803 -.204 -.317 -.204
17 500 403 243 243 257 160 512 369 252 251 269 126 0 0 150 162 76 85 90 55 75 40 417 395 1.606 .623 .468 .41 .331 4.014 52 323 .518 .25 90 3930 8140 37 46 264 273 0 282 170 112 .435 258 88 2.297 .328 -1.2 -1.61 -1.2
18 505 421 253 238 252 183 530 335 257 239 277 97 0 0 153 212 52 67 84 65 82 38 435 374 1.377 .726 .35 .481 .398 5.44 52 255 1.497 .2 80 4070 8150 39 47 279 287 0 294 166 128 .508 234 68 1.969 .245 -.978 -2.03 -.978
19 964 1799 246 236 718 1563 1018 1854 268 249 772 1618 0 0 272 441 237 114 92 100 80 100 2281 2390 .459 2.177 2.096 2.3 2.184 1.496 80 386 1.712 .54 100 4230 8150 38 48 294 304 0 1258 165 1093 1.522 1297 1131 .657 1.466 .606 .552 .606
20 491 534 257 221 234 313 522 466 252 233 265 245 0 0 157 220 54 73 81 93 75 71 547 510 .748 1.338 .925 1.309 .829 4.402 32 198 1.978 .26 70 4370 8140 38 45 309 316 0 373 155 219 .935 326 171 1.069 .647 -.096 -.629 -.096

Total number of rows: 43008

Table truncated, full table size 9291 Kbytes.




Supplementary data files not provided
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