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Sample GSM39932 Query DataSets for GSM39932
Status Public on Feb 21, 2005
Title Seminal vesicle 0235
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Seminal vesicle 0235
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-10/34530.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 GPL1824
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
1 834 829 289 575 545 254 958 918 315 549 669 343 0 0 439 391 194 252 73 53 67 38 799 1012 2.146 .466 .513 .638 .695 3.552 52 296 .789 .5 80 1810 8840 44 52 53 61 0 619 429 190 .348 685 256 2.875 .383 -1.524 -1.386 -1.524
2 926 677 274 513 652 164 972 692 331 504 698 179 0 0 462 349 308 385 76 25 57 1 816 877 3.976 .252 .256 .362 .328 2.53 52 246 .582 .24 80 1950 8840 44 52 67 75 0 505 383 122 .188 516 134 5.327 .191 -2.413 -2.386 -2.413
3 1956 5210 269 539 1687 4671 2276 5931 313 530 2007 5392 0 0 991 2687 279 410 83 90 82 86 6358 7399 .361 2.769 2.687 2.349 2.461 3.446 80 354 4.197 .6 100 2100 8850 44 54 81 91 0 3888 402 3486 2.066 4426 4024 .484 2.005 1.047 1.004 1.047
4 4260 24278 268 535 3992 23743 3419 25075 324 530 3151 24540 0 0 2759 16683 335 429 96 94 88 90 27735 27691 .168 5.948 7.788 4.536 5.709 3.653 52 266 7.276 .8 90 2240 8860 45 54 95 104 0 18118 399 17719 4.439 18713 18313 .225 5.812 2.15 2.539 2.15
5 1083 1163 288 539 795 624 1085 1222 360 544 797 683 0 0 635 517 337 356 80 73 65 46 1419 1480 1.274 .785 .857 .896 .879 2.504 52 257 .883 .68 80 2380 8840 44 52 110 118 -50 868 402 466 .586 912 510 1.707 .64 -.645 -.772
6 817 646 165 355 652 291 881 752 315 454 716 397 0 0 381 309 328 457 78 36 51 0 943 1113 2.241 .446 .554 .677 .544 2.392 52 266 1.11 .4 80 2530 8840 44 52 125 133 -100 482 265 217 .333 561 296 3.002 .414 -1.273 -1.586
7 1601 2396 103 128 1498 2268 1826 2631 274 390 1723 2503 0 0 529 842 332 467 94 96 88 90 3766 4226 .66 1.514 1.453 1.523 1.507 1.631 52 242 1.735 .76 80 2680 8850 45 53 140 148 0 1788 96 1693 1.13 1963 1868 .885 1.084 .176 .117 .176
8 8372 22583 296 574 8076 22009 9296 22375 343 528 9000 21801 0 0 4425 12665 260 386 93 98 93 97 30085 30801 .367 2.725 2.422 2.218 2.352 2.37 80 392 3.256 .84 110 2820 8850 43 54 152 163 0 16853 428 16425 2.034 16698 16269 .492 1.808 1.024 .854 1.024
9 1297 2302 273 564 1024 1738 1346 2472 347 549 1073 1908 0 0 791 1042 312 428 76 82 73 78 2762 2981 .589 1.697 1.778 1.346 1.462 2.63 52 233 2.119 .54 80 2960 8860 46 54 168 176 0 1718 421 1297 1.267 1845 1424 .79 1.327 .341 .408 .341
10 514 667 331 597 183 70 481 579 376 619 150 -18 0 0 247 274 267 327 32 19 9 3 253 132 2.614 .383 null 1.142 1.123 3.14 52 257 2.37 .23 80 3110 8840 44 52 183 191 -50 498 446 52 .285 432 null 3.503 null null -1.809
11 3070 5164 359 598 2711 4566 3421 5773 416 646 3062 5175 0 0 1303 1964 256 309 90 93 87 91 7277 8237 .594 1.684 1.69 1.629 1.697 2.546 80 413 1.949 .73 100 3260 8850 44 54 197 207 0 3854 446 3407 1.257 4308 3862 .796 1.261 .33 .335 .33
12 2609 2583 385 719 2224 1864 2456 2420 481 785 2071 1701 0 0 733 1234 349 419 100 83 91 83 4088 3772 1.193 .838 .821 .816 .794 2.478 12 104 1.271 .54 50 3420 8840 45 50 215 220 0 1928 537 1391 .625 1806 1269 1.599 .613 -.677 -.706 -.677
13 1376 1744 342 597 1034 1147 1614 1863 390 574 1272 1266 0 0 580 793 243 311 84 84 81 71 2181 2538 .901 1.109 .995 1.168 1.116 2.511 32 161 1.781 .55 60 3540 8850 46 52 227 233 0 1301 446 856 .828 1390 945 1.208 .743 -.273 -.429 -.273
14 549 6418 297 535 252 5883 489 5008 340 548 192 4473 0 0 283 4749 215 254 42 92 25 90 6135 4665 .043 23.345 23.297 15.324 17.538 2.717 80 341 28.537 .58 100 3700 8850 44 54 241 251 0 4790 399 4390 17.422 3737 3338 .057 17.386 4.123 4.12 4.123
15 9207 21405 289 517 8918 20888 8898 24164 299 527 8609 23647 0 0 4894 14173 113 183 93 93 92 91 29806 32256 .427 2.342 2.747 1.406 2.236 5.049 80 385 3.019 .81 110 3840 8840 42 53 254 265 0 15974 386 15588 1.748 18033 17647 .572 2.05 .806 1.036 .806
16 2810 7936 306 522 2504 7414 3325 9056 325 541 3019 8534 0 0 1428 3514 129 211 90 94 90 92 9918 11553 .338 2.961 2.827 2.794 2.639 2.475 52 289 3.516 .74 90 3990 8850 44 53 270 279 0 5922 390 5533 2.21 6758 6369 .453 2.11 1.144 1.077 1.144
17 717 564 311 541 406 23 743 587 318 549 432 46 0 0 273 209 94 172 84 21 78 7 429 478 17.652 .057 .106 .29 .255 2.732 52 246 .37 .17 80 4140 8840 44 52 286 294 0 421 404 17 .042 438 34 23.654 .079 -4.564 -3.654 -4.564
18 764 499 318 525 446 -26 743 470 325 529 425 -55 0 0 390 165 83 140 82 13 75 3 420 370 null null null .33 .272 3.963 52 236 .196 .2 80 4280 8840 44 52 300 308 0 372 392 -19 null 351 null null null null null null
19 1675 3563 301 498 1374 3065 1914 3843 310 515 1613 3345 0 0 752 1166 88 160 90 97 88 96 4439 4958 .448 2.231 2.074 2.261 1.997 2.366 80 361 2.455 .72 100 4430 8850 44 54 314 324 0 2659 372 2287 1.665 2868 2496 .601 1.548 .735 .63 .735
20 606 529 296 503 310 26 641 551 314 496 345 48 0 0 278 167 105 153 78 21 65 3 336 393 11.923 .084 .139 .278 .304 3.706 52 225 -1 -1 80 4570 8840 44 52 329 337 -50 395 375 19 .063 411 36 15.977 .104 -3.268 -3.998

Total number of rows: 43008

Table truncated, full table size 9572 Kbytes.




Supplementary data files not provided
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