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Sample GSM39993 Query DataSets for GSM39993
Status Public on Feb 21, 2005
Title Gallbladder 2131
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Gallbladder 2131
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/36422.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 = 31.09; Parameter Scan Time = 12:52:21; Parameter PMT Volts = 675; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 44790; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 4.25; 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 = 31.09; Parameter Scan Time = 12:52:21; Parameter PMT Volts = 700; Parameter Scan Date = 2002-12-13; Parameter Pixel Size = 10; Parameter Laser on time = 263785; Parameter Focus Position = 0; Parameter Scanner Model = GenePix 4000B [81971]; Parameter Laser Power = 3.16; 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
1 869 411 276 154 593 257 899 419 281 164 623 265 0 0 244 146 67 62 96 88 94 80 850 888 2.307 .433 .425 .409 .433 1.597 52 228 .415 .82 80 1590 8240 60 68 39 47 0 449 168 280 .473 457 289 2.114 .464 -1.08 -1.107 -1.08
2 1108 1466 275 156 833 1310 1138 1523 280 164 863 1367 0 0 271 484 61 58 100 100 100 100 2143 2230 .636 1.573 1.584 1.56 1.561 1.243 52 312 1.579 .95 90 1740 8230 58 67 53 62 0 1600 170 1430 1.716 1662 1492 .583 1.729 .779 .79 .779
3 1698 1305 259 166 1439 1139 1657 1308 267 167 1398 1142 0 0 758 615 60 60 100 100 100 98 2578 2540 1.263 .792 .817 .761 .804 1.436 52 254 .795 .97 80 1890 8230 59 67 69 77 0 1424 181 1243 .864 1427 1246 1.158 .891 -.211 -.166 -.211
4 967 552 273 166 694 386 1002 523 280 174 729 357 0 0 312 244 72 65 100 94 98 88 1080 1086 1.798 .556 .49 .505 .529 1.949 52 243 .558 .82 80 2030 8230 59 67 83 91 0 602 181 421 .607 571 390 1.647 .534 -.72 -.904 -.72
5 1390 1914 298 171 1092 1743 1402 1929 306 178 1104 1758 0 0 336 559 64 63 100 100 100 100 2835 2862 .627 1.596 1.592 1.569 1.602 1.374 52 267 1.661 .93 80 2180 8230 59 67 98 106 0 2089 187 1902 1.742 2105 1919 .574 1.738 .801 .797 .801
6 985 480 308 169 677 311 1004 452 316 206 696 283 0 0 198 133 122 231 100 68 100 18 988 979 2.177 .459 .407 .434 .457 1.59 32 221 .586 .79 70 2320 8220 58 65 112 119 0 524 184 339 .501 493 309 1.995 .444 -.996 -1.172 -.996
7 2133 2028 300 172 1833 1856 1701 969 306 184 1401 797 0 0 3250 6955 69 68 100 100 100 100 3689 2198 .988 1.013 .569 .634 .585 1.56 52 272 2.029 .96 80 2480 8230 59 67 128 136 0 2213 188 2026 1.105 1057 870 .905 .621 .144 -.688 .144
8 1033 648 284 174 749 474 1095 616 380 340 811 442 0 0 334 250 886 1069 36 3 0 0 1223 1253 1.58 .633 .545 .624 .614 1.497 52 303 .726 .65 90 2620 8220 57 66 141 150 0 707 190 517 .691 672 482 1.448 .595 -.534 -.75 -.534
9 1176 573 270 163 906 410 1166 527 366 336 896 364 0 0 249 224 892 1076 50 0 0 0 1316 1260 2.21 .453 .406 .411 .447 1.535 52 300 .499 .89 90 2760 8230 58 67 155 164 0 625 178 447 .494 575 397 2.025 .443 -1.018 -1.173 -1.018
10 1098 661 274 160 824 501 996 641 279 171 722 481 0 0 479 251 75 73 100 100 100 96 1325 1203 1.645 .608 .666 .625 .643 1.526 32 207 .609 .85 70 2910 8220 58 65 171 178 0 721 175 547 .664 700 525 1.507 .727 -.592 -.46 -.592
11 1707 849 274 163 1433 686 1720 826 278 171 1446 663 0 0 320 231 70 66 100 100 100 100 2119 2109 2.089 .479 .459 .463 .462 1.421 52 329 .455 .9 90 3050 8230 58 67 184 193 0 927 178 749 .522 901 724 1.914 .5 -.937 -.999 -.937
12 2146 4646 286 170 1860 4476 2161 4394 304 230 1875 4224 0 0 844 2019 133 283 100 100 96 96 6336 6099 .416 2.406 2.253 2.426 2.396 1.263 32 208 2.35 .95 70 3200 8220 58 65 200 207 0 5070 186 4885 2.626 4795 4610 .381 2.459 1.393 1.298 1.393
13 981 650 261 165 720 485 974 605 281 197 713 440 0 0 265 256 107 215 98 96 98 51 1205 1153 1.485 .674 .617 .661 .628 1.416 80 371 .852 .79 100 3350 8220 57 67 214 224 0 709 180 529 .735 660 480 1.36 .673 -.444 -.57 -.444
14 1125 701 270 173 855 528 1143 646 308 235 873 473 0 0 386 257 445 831 87 13 47 0 1383 1346 1.619 .618 .542 .624 .609 1.796 80 314 .628 .85 100 3500 8220 57 67 229 239 0 765 189 576 .674 705 516 1.484 .591 -.569 -.758 -.569
15 1596 1480 283 178 1313 1302 1583 1495 293 186 1300 1317 0 0 365 313 73 66 100 100 100 100 2615 2617 1.008 .992 1.013 1.004 .982 1.271 80 305 .986 .95 100 3640 8220 57 67 243 253 0 1615 194 1421 1.082 1632 1437 .924 1.106 .114 .145 .114
16 4935 11186 282 171 4653 11015 5033 11570 289 180 4751 11399 0 0 1414 3296 76 67 100 100 98 100 15668 16150 .422 2.367 2.399 2.402 2.361 1.244 80 361 2.379 .99 100 3790 8220 57 67 258 268 0 12208 187 12021 2.583 12627 12440 .387 2.618 1.369 1.389 1.369
17 986 1241 285 173 701 1068 921 1162 289 181 636 989 0 0 312 380 67 62 100 100 100 100 1769 1625 .656 1.524 1.555 1.53 1.624 1.375 52 235 1.482 .9 80 3930 8220 58 66 273 281 0 1354 189 1166 1.663 1268 1079 .601 1.697 .734 .763 .734
18 993 697 307 187 686 510 931 675 319 201 624 488 0 0 463 243 83 82 100 100 91 91 1196 1112 1.345 .743 .782 .821 .811 1.404 12 104 .674 .85 50 4060 8220 59 64 287 292 0 761 204 557 .811 737 533 1.233 .853 -.302 -.229 -.302
19 2314 1512 275 168 2039 1344 2275 1503 291 196 2000 1335 0 0 445 256 119 169 100 100 100 100 3383 3335 1.517 .659 .668 .665 .635 1.274 52 341 .638 .94 90 4220 8210 56 65 301 310 0 1650 183 1467 .719 1640 1457 1.39 .728 -.475 -.457 -.475
20 1433 1480 297 167 1136 1313 1406 1525 312 188 1109 1358 0 0 315 292 154 125 100 100 98 100 2449 2467 .865 1.156 1.225 1.173 1.133 1.268 52 313 1.083 .94 90 4370 8210 56 65 316 325 0 1615 182 1433 1.261 1664 1482 .793 1.336 .335 .418 .335

Total number of rows: 43104

Table truncated, full table size 9488 Kbytes.




Supplementary data files not provided
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