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Sample GSM39996 Query DataSets for GSM39996
Status Public on Feb 21, 2005
Title Thyroid 0838
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Thyroid 0838
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36425.gif
Scanning parameters - Channel 1; Parameters for laser scanning of a hybridized array in channel 1.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 13:29:14; Parameter PMT Volts = 680; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 44827; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.34; Parameter Scan Power = 100; Parameter Scanning software version = 2.0.2.2; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
Scanning parameters - Channel 2; Parameters for laser scanning of a hybridized array in channel 2.; Protocol Type = Scanning parameters; Parameter Scanner Make = Axon Instruments (V1.00); Parameter Scan Temperature = 31.15; Parameter Scan Time = 13:29:14; Parameter PMT Volts = 700; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 263822; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.17; Parameter Scanning software version = 2.0.2.2; Parameter Scan Power = 100; Parameter Scanning software = AxImageIO; Performer: Radha,,Shyamsundar
 
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 GPL1826
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 1193 1262 427 534 766 728 1234 1308 441 563 807 774 0 0 184 274 134 215 100 96 100 81 1494 1581 1.052 .95 .959 .896 .972 1.532 32 188 1.138 .86 70 1730 8770 57 64 53 60 -100 1124 476 648 .847 1165 689 1.181 .854 -.227 -.24
2 3118 3660 457 589 2661 3071 1449 1262 476 624 992 673 0 0 6907 10197 136 235 98 92 96 76 5732 1665 .866 1.154 .678 .7 .689 2.024 52 265 1.714 .89 80 1870 8760 56 64 67 75 -100 3260 525 2736 1.028 1124 599 .973 .604 -.727 .04
3 2424 2751 459 577 1965 2174 2563 2862 479 610 2104 2285 0 0 488 553 126 244 100 100 100 100 4139 4389 .904 1.106 1.086 1.107 1.154 1.183 32 214 1.114 .97 70 2020 8760 56 63 82 89 0 2450 514 1937 .986 2549 2035 1.015 .967 -.021 -.048 -.021
4 1478 1482 446 520 1032 962 1452 1311 468 569 1006 791 0 0 317 429 127 204 100 100 100 100 1994 1797 1.073 .932 .786 .893 .863 1.344 32 206 .996 .91 70 2160 8760 56 63 96 103 0 1320 463 857 .83 1168 705 1.204 .7 -.268 -.514 -.268
5 1666 2184 448 541 1218 1643 1631 2244 459 578 1183 1703 0 0 311 304 119 201 100 100 100 100 2861 2886 .741 1.349 1.44 1.368 1.386 1.249 52 313 1.346 .93 90 2310 8760 55 64 110 119 0 1945 482 1464 1.202 1999 1517 .832 1.282 .265 .359 .265
6 1062 1364 443 529 619 835 1071 1345 457 562 628 816 0 0 189 307 130 227 100 100 98 88 1454 1444 .741 1.349 1.299 1.323 1.375 1.376 52 254 1.518 .87 80 2450 8750 55 63 125 133 0 1215 471 744 1.202 1198 727 .832 1.157 .265 .211 .265
7 1561 1906 445 536 1116 1370 1637 1958 468 598 1192 1422 0 0 332 405 139 291 100 100 98 96 2486 2614 .815 1.228 1.193 1.232 1.235 1.288 52 300 1.243 .92 90 2600 8760 55 64 139 148 0 1698 477 1220 1.094 1744 1267 .914 1.063 .129 .088 .129
8 1382 3007 435 488 947 2519 1407 3066 453 526 972 2578 0 0 279 550 122 174 100 100 100 100 3466 3550 .376 2.66 2.652 2.72 2.672 1.288 52 254 2.662 .94 80 2740 8760 56 64 154 162 0 2679 435 2244 2.369 2731 2296 .422 2.363 1.245 1.24 1.245
9 1190 988 421 479 769 509 1218 964 442 501 797 485 0 0 236 220 125 164 100 93 97 80 1278 1282 1.511 .662 .609 .603 .665 1.681 80 369 .726 .83 100 2890 8760 55 65 168 178 0 880 427 453 .59 859 432 1.696 .542 -.762 -.883 -.762
10 1055 1338 410 462 645 876 1047 1324 427 480 637 862 0 0 230 364 110 169 100 100 100 92 1521 1499 .736 1.358 1.353 1.313 1.33 1.386 52 220 1.466 .9 80 3040 8760 56 64 184 192 0 1192 412 780 1.21 1179 768 .827 1.205 .275 .27 .275
11 2305 4586 397 424 1908 4162 2417 4724 411 451 2020 4300 0 0 509 1084 104 143 100 100 100 100 6070 6320 .458 2.181 2.129 2.19 2.155 1.219 80 365 2.189 .98 100 3180 8760 55 65 197 207 0 4085 378 3707 1.943 4208 3830 .515 1.896 .958 .923 .958
12 6722 14709 395 416 6327 14293 5198 15131 402 444 4803 14715 0 0 7429 4959 91 155 100 100 100 100 20620 19518 .443 2.259 3.064 2.844 3.169 1.509 52 293 1.461 .73 90 3320 8760 55 64 211 220 0 13102 371 12732 2.012 13478 13108 .497 2.729 1.009 1.448 1.009
13 1366 1163 442 467 924 696 1417 1182 504 519 975 715 0 0 275 183 237 235 96 96 93 87 1620 1690 1.328 .753 .733 .767 .782 1.338 32 167 .774 .86 60 3460 8760 57 63 227 233 0 1036 416 620 .671 1053 637 1.49 .653 -.576 -.614 -.576
14 1083 1025 376 353 707 672 1158 953 368 376 782 600 0 0 253 597 281 290 90 88 78 53 1379 1382 1.052 .95 .767 .85 .832 1.61 52 276 1.201 .78 80 3630 8740 54 62 243 251 -50 913 314 599 .847 849 534 1.181 .683 -.549 -.24
15 1840 966 359 328 1481 638 1810 964 393 374 1451 636 0 0 955 383 434 485 90 76 82 11 2119 2087 2.321 .431 .438 .465 .459 1.619 52 257 .422 .91 80 3760 8760 56 64 256 264 0 860 292 568 .384 859 567 2.606 .39 -1.382 -1.357 -1.382
16 273 581 498 492 -225 89 78 105 1672 1819 -420 -387 0 0 552 1131 2285 2358 0 8 0 0 -136 -807 null null null 1.398 .976 3.658 12 104 .963 .95 50 3900 8750 56 61 271 276 -100 518 438 79 null 94 -345 null null null null
17 2228 4104 352 290 1876 3814 2265 4003 372 373 1913 3713 0 0 360 832 539 624 100 100 93 100 5690 5626 .492 2.033 1.941 2.035 1.946 1.245 32 232 1.981 .96 70 4050 8750 55 62 285 292 0 3656 258 3397 1.811 3566 3307 .552 1.729 .857 .79 .857
18 409 372 359 297 50 75 360 304 391 391 1 7 0 0 237 262 544 722 1 3 1 1 125 8 .667 1.5 7 .962 .994 2.801 52 282 1.003 .97 80 4210 8740 54 62 301 309 -50 331 265 67 1.336 271 6 .748 6.235 2.64 .418
19 3874 4918 356 285 3518 4633 4151 5199 349 299 3795 4914 0 0 1113 1380 113 218 100 100 100 100 8151 8709 .759 1.317 1.295 1.336 1.336 1.174 80 333 1.308 .99 100 4350 8760 55 65 314 324 0 4381 254 4127 1.173 4631 4377 .852 1.153 .23 .206 .23
20 2117 2143 355 283 1762 1860 2188 2195 359 288 1833 1912 0 0 763 783 63 81 100 100 100 100 3622 3745 .947 1.056 1.043 1.081 1.056 1.294 80 311 1.05 .98 100 4500 8760 55 65 329 339 0 1909 252 1657 .94 1955 1703 1.063 .929 -.089 -.106 -.089

Total number of rows: 43104

Table truncated, full table size 9733 Kbytes.




Supplementary data files not provided
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