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Sample GSM39985 Query DataSets for GSM39985
Status Public on Feb 21, 2005
Title Thyroid 0029
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Thyroid 0029
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-03/14877.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 GPL1825
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 1227 1388 443 331 784 1057 1333 1457 462 344 890 1126 0 0 339 486 128 141 92 90 88 88 1841 2016 .742 1.348 1.265 1.315 1.335 1.402 52 285 1.333 .9 90 810 8520 79 88 48 57 -100 1021 243 777 .991 1071 828 1.009 .93 -.104 -.013
2 1396 1682 443 334 953 1348 1364 1640 440 338 921 1306 0 0 471 547 84 88 100 100 91 100 2301 2227 .707 1.414 1.418 1.558 1.457 1.64 12 72 1.415 .91 50 970 8520 81 86 66 71 0 1237 246 991 1.04 1206 960 .961 1.043 .057 .06 .057
3 3380 2991 429 371 2951 2620 3588 3143 432 378 3159 2772 0 0 868 832 76 106 98 100 98 100 5571 5931 1.126 .888 .877 .889 .876 1.391 80 319 .894 .97 110 1090 8520 78 89 75 86 0 2199 273 1926 .653 2311 2038 1.532 .645 -.615 -.632 -.615
4 1360 1957 423 421 937 1536 1466 2108 427 434 1043 1687 0 0 503 917 65 105 93 87 93 81 2473 2730 .61 1.639 1.617 1.411 1.719 2.752 32 73 1.674 .91 60 1240 8530 82 88 93 99 0 1439 310 1129 1.205 1550 1240 .83 1.189 .269 .25 .269
5 1541 1857 411 413 1130 1444 1491 1819 415 412 1080 1406 0 0 312 301 72 103 100 100 100 100 2574 2486 .783 1.278 1.302 1.3 1.266 1.275 80 263 1.361 .92 100 1360 8520 79 89 103 113 0 1365 304 1062 .94 1338 1034 1.064 .957 -.09 -.063 -.09
6 1409 2619 407 355 1002 2264 1455 2739 416 382 1048 2384 0 0 355 802 110 185 100 100 100 100 3266 3432 .443 2.259 2.275 2.23 2.373 1.673 12 70 2.339 .92 50 1500 8520 81 86 119 124 0 1926 261 1665 1.661 2014 1753 .602 1.673 .732 .742 .732
7 1569 2231 409 370 1160 1861 1475 1810 431 407 1066 1440 0 0 905 3414 111 206 98 98 97 96 3021 2506 .623 1.604 1.351 1.373 1.295 1.511 80 208 3.294 .87 100 1620 8520 79 89 129 139 -100 1640 272 1368 1.18 1331 1059 .848 .993 -.01 .238
8 750 1045 411 352 339 693 484 514 510 518 73 162 0 0 433 817 290 466 41 43 37 42 1032 235 .489 2.044 2.219 1.77 1.824 2.338 80 247 1.944 .92 100 1730 8480 75 85 140 150 -50 768 259 510 1.503 378 119 .665 1.632 .706 .588
9 708 766 406 329 302 437 542 486 480 455 136 157 0 0 353 534 262 417 41 38 22 26 739 293 .691 1.447 1.154 1.463 1.341 2.245 80 297 1.682 .9 100 1870 8480 75 85 154 164 -50 563 242 321 1.064 357 115 .94 .849 -.236 .089
10 1312 1477 401 311 911 1166 1313 1506 409 323 912 1195 0 0 196 373 72 104 100 98 100 98 2077 2107 .781 1.28 1.31 1.219 1.27 1.493 80 278 1.36 .91 100 2040 8490 76 86 171 181 0 1086 229 857 .941 1107 879 1.063 .963 -.088 -.054 -.088
11 1855 10204 369 282 1486 9922 1992 10469 379 292 1623 10187 0 0 524 2272 77 96 100 100 100 100 11408 11810 .15 6.677 6.277 7.11 6.438 1.486 80 258 6.651 .95 100 2160 8480 75 85 183 193 0 7503 207 7296 4.91 7698 7490 .204 4.615 2.296 2.206 2.296
12 1774 2736 361 280 1413 2456 1862 2771 362 283 1501 2491 0 0 315 611 62 78 100 100 100 100 3869 3992 .575 1.738 1.66 1.718 1.779 1.339 52 235 1.822 .95 90 2300 8480 75 84 197 206 0 2012 206 1806 1.278 2038 1832 .782 1.22 .354 .287 .354
13 1434 2081 369 289 1065 1792 1439 2121 371 298 1070 1832 0 0 307 315 61 79 100 100 100 100 2857 2902 .594 1.683 1.712 1.735 1.704 1.319 52 232 1.654 .92 90 2440 8490 76 85 211 220 0 1530 213 1318 1.237 1560 1347 .808 1.259 .307 .332 .307
14 1576 2273 374 291 1202 1982 1582 2237 381 302 1208 1946 0 0 267 433 67 82 100 100 100 100 3184 3154 .606 1.649 1.611 1.657 1.614 1.235 52 237 1.672 .94 90 2580 8490 76 85 225 234 0 1671 214 1457 1.212 1645 1431 .825 1.185 .278 .244 .278
15 1841 2689 402 319 1439 2370 1859 2758 405 324 1457 2439 0 0 322 558 71 101 100 100 100 100 3809 3896 .607 1.647 1.674 1.642 1.64 1.258 52 225 1.691 .95 90 2720 8470 74 83 239 248 -100 1977 235 1743 1.211 2028 1793 .826 1.231 .3 .276
16 1704 1989 422 344 1282 1645 1722 1973 426 352 1300 1629 0 0 261 333 74 91 100 100 100 100 2927 2929 .779 1.283 1.253 1.29 1.249 1.225 80 281 1.28 .95 110 2830 8490 75 86 249 260 0 1463 253 1210 .943 1451 1198 1.06 .921 -.084 -.118 -.084
17 1491 2089 421 362 1070 1727 1528 2114 425 368 1107 1752 0 0 276 357 77 102 100 100 100 100 2797 2859 .62 1.614 1.583 1.651 1.687 1.282 52 244 1.588 .94 90 2960 8470 74 83 263 272 0 1536 266 1270 1.187 1554 1288 .843 1.164 .247 .219 .247
18 1029 937 435 372 594 565 1012 879 440 383 577 507 0 0 169 288 88 113 100 96 100 88 1159 1084 1.051 .951 .879 .851 .918 1.712 52 242 1.16 .8 90 3100 8470 74 83 277 286 0 689 274 415 .699 646 373 1.43 .646 -.516 -.63 -.516
19 1323 1956 434 383 889 1573 1334 1936 440 387 900 1553 0 0 190 398 88 110 100 100 100 100 2462 2453 .565 1.769 1.726 1.754 1.732 1.234 52 242 1.794 .94 90 3220 8480 75 84 289 298 0 1438 282 1157 1.301 1424 1142 .769 1.269 .38 .343 .38
20 2037 2974 405 344 1632 2630 2075 3001 405 350 1670 2657 0 0 472 1026 74 102 100 100 100 100 4262 4327 .621 1.612 1.591 1.534 1.587 1.435 80 291 1.714 .95 100 3380 8490 76 86 305 315 0 2187 253 1934 1.185 2207 1954 .844 1.17 .245 .226 .245

Total number of rows: 44160

Table truncated, full table size 9984 Kbytes.




Supplementary data files not provided
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