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Sample GSM39995 Query DataSets for GSM39995
Status Public on Feb 21, 2005
Title Thyroid 0182
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Thyroid 0182
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36424.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 = 31.12; Parameter Scan Time = 13:14:41; Parameter PMT Volts = 700; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 44812; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.31; 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 = 31.12; Parameter Scan Time = 13:14:41; Parameter PMT Volts = 685; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 263808; 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) [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 1240 464 111 101 1129 363 1285 476 305 153 1174 375 0 0 168 141 403 135 100 100 100 66 1492 1549 3.11 .322 .319 .303 .313 1.332 12 72 .311 .9 50 1810 8250 62 67 62 67 0 476 104 373 .33 489 385 3.031 .328 -1.6 -1.609 -1.6
2 1659 499 206 130 1453 369 1854 558 268 148 1648 428 0 0 669 241 211 87 87 81 87 78 1822 2076 3.938 .254 .26 .263 .247 1.747 32 227 .276 .92 70 1970 8240 60 67 77 84 0 512 133 379 .261 573 439 3.837 .267 -1.94 -1.908 -1.94
3 2237 2195 225 139 2012 2056 2414 2368 252 150 2189 2229 0 0 1037 1105 160 77 96 100 90 96 4068 4418 .979 1.022 1.018 .991 .988 1.573 52 278 1.077 .96 80 2120 8250 61 69 92 100 0 2253 143 2110 1.049 2430 2288 .954 1.045 .069 .064 .069
4 1109 427 172 110 937 317 1099 433 214 129 927 323 0 0 617 204 152 74 87 84 84 78 1254 1250 2.956 .338 .348 .323 .34 1.458 32 165 .341 .9 60 2260 8240 61 67 107 113 0 438 113 325 .347 444 331 2.88 .358 -1.526 -1.484 -1.526
5 1898 1963 126 101 1772 1862 2073 2154 281 217 1947 2053 0 0 581 816 392 392 100 93 93 90 3634 4000 .952 1.051 1.054 .976 1.03 1.314 32 223 1.105 .96 70 2400 8250 61 68 120 127 0 2015 104 1911 1.078 2211 2107 .927 1.082 .109 .114 .109
6 1237 351 149 108 1088 243 1280 342 271 177 1131 234 0 0 729 180 313 301 84 31 81 6 1331 1365 4.477 .223 .207 .244 .217 2.02 32 172 .235 .91 60 2550 8250 62 68 136 142 0 360 111 249 .229 351 240 4.363 .212 -2.125 -2.236 -2.125
7 1449 997 188 125 1261 872 1680 941 240 133 1492 816 0 0 663 510 175 71 90 93 84 90 2133 2308 1.446 .692 .547 .699 .656 1.923 32 167 .695 .92 60 2710 8250 62 68 152 158 0 1023 128 895 .71 966 837 1.409 .561 -.495 -.833 -.495
8 757 1184 233 151 524 1033 854 1369 335 366 621 1218 0 0 577 953 358 607 58 58 50 50 1557 1839 .507 1.971 1.961 1.364 1.739 3.591 12 100 1.774 .95 50 2820 8240 61 66 163 168 0 1215 155 1060 2.023 1405 1250 .494 2.013 1.017 1.009 1.017
9 467 193 156 110 311 83 116 125 222 155 -40 15 0 0 543 151 187 177 38 23 30 5 394 -25 3.747 .267 null .306 .343 2.454 52 274 .26 .87 80 3010 8240 60 68 181 189 -50 198 113 85 .274 128 15 3.651 null null -1.868
10 83 80 103 94 -20 -14 81 76 181 136 -22 -18 0 0 26 27 281 193 0 0 0 0 -34 -40 null null null 1.105 1 4.62 52 310 .661 .96 80 3160 8240 60 68 196 204 -50 82 96 -14 null 78 -18 null null null null
11 2277 2092 90 88 2187 2004 2365 2045 103 93 2275 1957 0 0 714 784 58 38 100 100 100 100 4191 4232 1.091 .916 .86 .881 .902 1.197 12 92 .949 .97 50 3330 8260 63 68 214 219 0 2147 90 2057 .94 2099 2008 1.063 .883 -.089 -.18 -.089
12 2591 9181 93 79 2498 9102 2774 8397 112 90 2681 8318 0 0 1899 6839 72 46 92 98 88 96 11600 10999 .274 3.644 3.103 3.581 3.662 1.561 52 253 3.676 .97 80 3440 8250 61 69 224 232 0 9422 81 9341 3.739 8618 8536 .267 3.184 1.903 1.671 1.903
13 1113 563 96 79 1017 484 1149 583 131 94 1053 504 0 0 455 197 99 50 98 100 96 98 1501 1557 2.101 .476 .479 .488 .478 1.627 52 302 .406 .89 90 3590 8250 60 69 238 247 0 578 81 497 .488 598 517 2.047 .491 -1.034 -1.026 -1.034
14 1015 372 92 79 923 293 963 358 130 94 871 279 0 0 490 119 103 50 100 97 100 97 1216 1150 3.15 .317 .32 .319 .321 1.474 80 332 .271 .88 100 3740 8260 61 71 253 263 0 382 81 301 .326 367 286 3.07 .329 -1.618 -1.605 -1.618
15 1818 466 88 83 1730 383 1899 479 149 108 1811 396 0 0 391 112 229 104 100 100 100 92 2113 2207 4.517 .221 .219 .217 .226 1.329 52 293 .209 .89 90 3870 8260 61 70 266 275 0 478 85 393 .227 492 406 4.401 .224 -2.138 -2.156 -2.138
16 5493 11391 108 98 5385 11293 6595 13436 204 128 6487 13338 0 0 2987 6310 221 99 93 95 92 95 16678 19825 .477 2.097 2.056 1.991 2.074 1.348 80 435 2.136 .99 110 4020 8260 60 71 280 291 0 11690 101 11590 2.152 13789 13688 .465 2.11 1.106 1.077 1.106
17 1454 1094 323 140 1131 954 1403 1073 460 286 1080 933 0 0 250 219 537 368 100 100 50 91 2085 2013 1.186 .844 .864 .842 .854 1.224 12 99 .731 .95 50 4150 8250 62 67 296 301 0 1123 144 979 .866 1101 958 1.155 .887 -.208 -.174 -.208
18 1170 669 291 138 879 531 382 159 299 145 91 21 0 0 2964 1643 316 76 21 34 11 21 1410 112 1.655 .604 .231 .555 .488 2.532 52 258 .477 .92 80 4330 8240 60 68 313 321 -50 687 142 545 .62 163 22 1.613 .237 -2.078 -.69
19 2580 2981 285 139 2295 2842 3160 3508 355 166 2875 3369 0 0 1436 1781 472 134 84 84 78 84 5137 6244 .808 1.238 1.172 .988 1.172 1.802 52 220 1.217 .98 80 4460 8260 62 70 326 334 0 3059 143 2917 1.271 3600 3457 .787 1.203 .346 .266 .346
20 1792 1697 302 156 1490 1541 1741 1673 370 200 1439 1517 0 0 1514 1008 417 184 82 86 73 78 3031 2956 .967 1.034 1.054 1.026 1.114 1.764 52 296 .587 .71 90 4610 8260 61 70 340 349 -100 1742 160 1581 1.061 1717 1557 .942 1.082 .114 .086

Total number of rows: 43104

Table truncated, full table size 9669 Kbytes.




Supplementary data files not provided
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