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Sample GSM39997 Query DataSets for GSM39997
Status Public on Feb 21, 2005
Title Thyroid 1193
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Thyroid 1193
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36426.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 = 29.62; Parameter Scan Time = 10:09:26; Parameter PMT Volts = 685; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 45069; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.42; 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 = 29.62; Parameter Scan Time = 10:09:26; Parameter PMT Volts = 700; Parameter Scan Date = 2002-12-14; Parameter Pixel Size = 10; Parameter Laser on time = 264064; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.07; 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) [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 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
1 520 391 211 117 309 274 495 379 214 120 284 262 0 0 142 105 53 39 98 100 92 100 583 546 1.128 .887 .923 .933 .854 1.695 52 241 .796 .8 80 1680 8350 79 87 72 80 0 400 120 280 .908 388 268 1.102 .944 -.14 -.083 -.14
2 843 443 213 121 630 322 888 454 212 125 675 333 0 0 198 148 54 43 100 100 100 92 952 1008 1.957 .511 .493 .473 .482 1.521 52 254 .502 .87 80 1810 8330 77 85 85 93 0 453 124 330 .523 465 341 1.912 .505 -.935 -.986 -.935
3 1081 865 208 116 873 749 996 824 217 120 788 708 0 0 344 277 51 36 100 100 100 100 1622 1496 1.166 .858 .898 .859 .877 1.282 32 224 .855 .94 70 1960 8330 77 84 100 107 0 885 119 767 .878 843 725 1.139 .92 -.188 -.121 -.188
4 549 379 208 123 341 256 552 395 212 124 344 272 0 0 97 89 55 42 100 100 96 100 597 616 1.332 .751 .791 .734 .796 1.462 32 204 .725 .76 70 2110 8330 77 84 115 122 0 388 126 262 .768 404 278 1.302 .809 -.38 -.305 -.38
5 888 860 220 131 668 729 889 860 222 135 669 729 0 0 184 262 55 48 100 100 100 100 1397 1398 .916 1.091 1.09 1.045 1.053 1.439 52 329 1.128 .92 90 2240 8330 76 85 127 136 0 880 134 746 1.117 880 746 .895 1.115 .159 .157 .159
6 530 370 216 128 314 242 521 376 222 139 305 248 0 0 104 86 53 77 100 100 100 82 556 553 1.298 .771 .813 .76 .848 1.623 52 262 .714 .79 80 2400 8330 77 85 144 152 0 379 131 248 .789 385 254 1.268 .832 -.342 -.265 -.342
7 841 660 202 124 639 536 856 673 206 129 654 549 0 0 233 180 49 40 100 100 98 100 1175 1203 1.192 .839 .839 .87 .818 1.406 52 242 .802 .92 80 2540 8340 78 86 158 166 0 675 127 549 .858 689 562 1.165 .859 -.22 -.219 -.22
8 668 799 215 124 453 675 671 811 226 133 456 687 0 0 159 215 103 72 98 100 98 100 1128 1143 .671 1.49 1.507 1.51 1.357 1.566 52 300 1.48 .82 90 2690 8330 76 85 172 181 0 818 127 691 1.525 830 703 .656 1.542 .609 .625 .609
9 594 415 219 129 375 286 579 412 225 143 360 283 0 0 129 135 67 95 100 92 96 77 661 643 1.311 .763 .786 .698 .794 1.78 80 362 .761 .84 100 2830 8330 76 86 186 196 0 425 132 293 .781 422 290 1.281 .805 -.357 -.314 -.357
10 524 398 216 127 308 271 508 383 220 135 292 256 0 0 117 114 55 51 100 100 100 96 579 548 1.137 .88 .877 .857 .829 1.683 52 233 .881 .79 80 2980 8330 77 85 202 210 0 407 130 277 .9 392 262 1.111 .897 -.151 -.156 -.151
11 1329 1455 222 134 1107 1321 1414 1535 222 146 1192 1401 0 0 411 478 52 77 98 100 98 100 2428 2593 .838 1.193 1.175 1.219 1.227 1.381 80 340 1.177 .96 100 3130 8340 77 87 216 226 0 1489 137 1352 1.221 1571 1434 .819 1.203 .288 .266 .288
12 2037 6768 212 129 1825 6639 2180 6897 213 147 1968 6768 0 0 782 2518 51 87 100 100 100 100 8464 8736 .275 3.638 3.439 3.766 3.808 1.383 52 232 3.673 .96 80 3280 8330 77 85 232 240 0 6927 132 6794 3.723 7059 6927 .269 3.52 1.896 1.815 1.896
13 636 531 211 127 425 404 648 522 215 136 437 395 0 0 152 158 53 45 100 100 97 95 829 832 1.052 .951 .904 .924 .935 1.609 80 340 .946 .88 100 3420 8330 76 86 245 255 0 543 130 413 .973 534 404 1.028 .925 -.04 -.112 -.04
14 568 393 209 129 359 264 564 383 212 133 355 254 0 0 125 95 48 44 100 100 100 98 623 609 1.36 .735 .715 .734 .681 1.599 52 276 .703 .8 90 3570 8330 76 85 260 269 0 402 132 270 .753 392 260 1.329 .732 -.41 -.45 -.41
15 1122 606 216 132 906 474 1152 615 222 138 936 483 0 0 227 132 52 48 100 100 100 100 1380 1419 1.911 .523 .516 .52 .529 1.396 80 345 .502 .91 100 3710 8330 76 86 274 284 0 620 135 485 .535 629 494 1.868 .528 -.901 -.921 -.901
16 4928 9641 213 132 4715 9509 4912 9606 220 142 4699 9474 0 0 1444 2805 82 86 100 100 100 100 14224 14173 .496 2.017 2.016 2.02 1.994 1.223 80 404 2.025 .98 110 3860 8330 75 86 288 299 0 9867 135 9732 2.064 9831 9696 .484 2.063 1.045 1.045 1.045
17 813 800 205 128 608 672 798 812 219 145 593 684 0 0 186 186 101 109 100 100 100 100 1280 1277 .905 1.105 1.153 1.115 1.126 1.328 52 230 1.063 .92 80 4000 8330 77 85 304 312 0 819 131 688 1.131 831 700 .884 1.18 .178 .239 .178
18 306 198 205 116 101 82 257 165 212 122 52 49 0 0 157 117 60 42 42 50 26 40 183 101 1.232 .812 .942 1.069 .906 2.278 52 235 .677 .73 80 4150 8320 76 84 319 327 -50 203 119 84 .831 169 50 1.204 .964 -.052 -.267
19 1744 2488 196 121 1548 2367 1789 2677 204 130 1593 2556 0 0 509 759 53 58 100 100 100 100 3915 4149 .654 1.529 1.605 1.535 1.537 1.338 80 339 1.54 .96 100 4290 8330 76 86 332 342 0 2546 124 2422 1.565 2740 2616 .639 1.642 .646 .716 .646
20 1005 995 202 126 803 869 1010 988 207 132 808 862 0 0 198 254 56 52 100 100 100 100 1672 1670 .924 1.082 1.067 1.062 1.056 1.277 52 280 1.061 .95 90 4430 8320 75 84 346 355 0 1018 129 889 1.108 1011 882 .903 1.092 .147 .127 .147

Total number of rows: 43104

Table truncated, full table size 9449 Kbytes.




Supplementary data files not provided
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