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Sample GSM39953 Query DataSets for GSM39953
Status Public on Feb 21, 2005
Title Parathyroid 2995
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Parathyroid 2995
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-10/34528.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
1 448 609 153 504 295 105 482 574 190 958 329 70 0 0 195 386 114 995 76 1 65 0 400 399 2.81 .356 .213 1.095 .895 4.182 52 268 15.825 .28 80 1660 8300 46 54 54 62 -50 564 467 97 .33 531 65 3.034 .197 -2.344 -1.601
2 339 209 109 77 230 132 353 213 138 341 244 136 0 0 110 65 94 685 86 0 65 0 362 380 1.742 .574 .557 .613 .562 1.862 52 289 21.841 .16 90 1810 8310 46 55 68 77 0 194 71 122 .531 197 126 1.882 .516 -.912 -.954 -.912
3 1771 2296 104 69 1667 2227 1969 2748 147 111 1865 2679 0 0 649 1022 138 143 100 97 98 95 3894 4544 .749 1.336 1.436 1.222 1.341 1.626 80 419 1.441 .93 110 1960 8300 44 55 82 93 0 2126 64 2062 1.237 2544 2481 .808 1.33 .307 .411 .307
4 2964 8434 100 63 2864 8371 2688 7907 116 75 2588 7844 0 0 2305 6624 90 81 100 97 91 92 11235 10432 .342 2.923 3.031 2.477 2.534 3.034 80 342 3.352 .84 100 2100 8300 45 55 97 107 0 7809 58 7751 2.706 7321 7263 .37 2.806 1.436 1.489 1.436
5 471 874 99 62 372 812 508 974 100 65 409 912 0 0 139 314 23 18 100 100 98 100 1184 1321 .458 2.183 2.23 2.181 2.139 1.628 52 290 2.671 .85 90 2240 8300 45 54 111 120 0 809 57 752 2.021 902 844 .495 2.065 1.015 1.046 1.015
6 331 239 99 61 232 178 294 250 102 65 195 189 0 0 162 89 23 26 90 90 84 86 410 384 1.303 .767 .969 .98 .777 3.676 52 265 .633 .76 80 2390 8300 46 54 127 135 0 221 56 165 .71 231 175 1.408 .897 -.493 -.156 -.493
7 837 844 103 66 734 778 902 979 113 83 799 913 0 0 283 304 51 92 100 98 94 96 1512 1712 .943 1.06 1.143 1.054 1.091 2.208 52 315 1.134 .87 90 2530 8300 45 54 140 149 0 781 61 720 .981 906 845 1.019 1.058 -.027 .081 -.027
8 5408 6045 106 67 5302 5978 5865 6973 117 81 5759 6906 0 0 2238 3000 53 79 100 100 100 98 11280 12665 .887 1.127 1.199 1.019 1.129 1.959 80 485 1.301 .87 110 2680 8290 43 54 154 165 0 5597 62 5535 1.044 6456 6394 .958 1.11 .062 .151 .062
9 904 698 103 67 801 631 932 615 109 73 829 548 0 0 403 317 41 38 96 98 94 98 1432 1377 1.269 .788 .661 .893 .844 2.391 52 335 .745 .83 90 2830 8300 45 54 170 179 0 646 62 584 .729 569 507 1.371 .612 -.455 -.708 -.455
10 322 200 109 70 213 130 379 192 110 73 270 122 0 0 137 84 28 26 83 91 83 75 343 392 1.638 .61 .452 .526 .631 1.967 12 98 .544 .67 50 2980 8290 46 51 187 192 0 185 65 120 .565 178 113 1.77 .418 -.823 -1.257 -.823
11 1843 2924 106 67 1737 2857 1985 3211 108 72 1879 3144 0 0 499 947 28 26 100 100 100 100 4594 5023 .608 1.645 1.673 1.605 1.653 1.311 80 454 1.778 .94 110 3130 8290 43 54 199 210 0 2707 62 2645 1.523 2973 2911 .657 1.549 .607 .632 .607
12 808 934 105 67 703 867 641 687 225 205 536 620 0 0 520 666 1243 1302 15 23 0 0 1570 1156 .811 1.233 1.157 1.251 1.183 2.055 52 223 1.299 .88 80 3260 8300 46 54 214 222 -100 865 62 803 1.142 636 574 .876 1.071 .099 .191
13 590 607 103 67 487 540 577 573 420 181 474 506 0 0 319 381 3646 1101 0 10 0 0 1027 980 .902 1.109 1.068 1.113 1.119 2.089 80 366 .177 .65 100 3410 8300 45 55 228 238 0 562 62 500 1.027 531 469 .974 .988 .038 -.017 .038
14 289 141 102 68 187 73 309 138 106 69 207 70 0 0 128 39 27 20 81 90 81 78 260 277 2.562 .39 .338 .403 .333 2.625 32 206 .331 .72 70 3560 8300 46 53 244 251 0 131 63 68 .361 128 65 2.767 .313 -1.468 -1.675 -1.468
15 2991 14048 97 64 2894 13984 2950 14671 103 67 2853 14607 0 0 1590 8277 34 22 100 100 97 100 16878 17460 .207 4.832 5.12 4.814 4.689 2.473 80 401 5.233 .94 100 3710 8300 45 55 258 268 0 13007 59 12948 4.474 13584 13525 .224 4.741 2.162 2.245 2.162
16 1541 5508 97 62 1444 5446 1677 6179 102 73 1580 6117 0 0 599 2310 46 101 100 100 98 100 6890 7697 .265 3.771 3.872 3.741 3.814 1.392 52 307 3.902 .94 90 3840 8290 44 53 271 280 0 5100 57 5043 3.492 5721 5664 .286 3.585 1.804 1.842 1.804
17 273 173 99 65 174 108 280 170 103 75 181 105 0 0 97 45 46 101 88 55 82 1 282 286 1.611 .621 .58 .632 .55 1.786 52 311 .498 .79 90 4000 8300 45 54 287 296 0 160 60 100 .575 157 97 1.74 .537 -.799 -.897 -.799
18 272 137 96 61 176 76 280 125 99 64 184 64 0 0 86 53 22 20 90 94 90 82 252 248 2.316 .432 .348 .414 .379 2.609 52 323 .388 .65 90 4140 8290 44 53 301 310 0 127 56 70 .4 116 59 2.501 .322 -1.323 -1.635 -1.323
19 946 1642 98 66 848 1576 965 1806 102 71 867 1740 0 0 298 584 29 24 100 100 100 100 2424 2607 .538 1.858 2.007 1.822 1.859 1.5 80 459 1.992 .92 110 4300 8280 42 53 316 327 0 1520 61 1459 1.721 1672 1611 .581 1.858 .783 .894 .783
20 287 161 101 64 186 97 310 133 103 68 209 69 0 0 92 96 24 23 94 96 90 76 283 278 1.918 .522 .33 .501 .416 3.05 52 225 .423 .44 80 4440 8290 45 53 332 340 0 149 59 90 .483 123 64 2.071 .306 -1.05 -1.71 -1.05

Total number of rows: 43008

Table truncated, full table size 9029 Kbytes.




Supplementary data files not provided
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