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Sample GSM39892 Query DataSets for GSM39892
Status Public on Feb 21, 2005
Title Ovary 1080
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Ovary 1080
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-01/24462.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 GPL1823
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
1 306 772 165 101 141 671 299 817 173 106 134 716 0 0 90 239 83 59 80 100 28 96 812 850 .21 4.759 5.343 4.724 4.986 2.072 52 355 4.595 .53 90 1460 7990 66 75 33 42 0 465 61 404 2.867 492 431 .349 3.219 1.519 1.687 1.519
2 311 229 174 97 137 132 306 226 177 100 132 129 0 0 92 62 45 24 86 100 69 90 269 261 1.038 .964 .977 .903 .872 2.125 52 242 .695 .62 80 1600 7990 67 75 48 56 0 138 58 80 .58 136 78 1.723 .589 -.785 -.764 -.785
3 740 572 166 104 574 468 773 633 170 106 607 529 0 0 225 216 45 25 100 100 98 98 1042 1136 1.226 .815 .871 .764 .781 1.895 52 310 .811 .88 90 1730 7990 66 75 60 69 0 345 63 282 .491 381 319 2.036 .525 -1.026 -.93 -1.026
4 1982 5851 168 109 1814 5742 2112 6240 175 113 1944 6131 0 0 724 2530 58 55 100 100 100 100 7556 8075 .316 3.165 3.154 3.018 3.256 1.836 52 322 3.468 .92 90 1890 7990 66 75 76 85 0 3525 66 3459 1.907 3759 3693 .524 1.9 .931 .926 .931
5 417 678 172 106 245 572 389 743 179 111 217 637 0 0 158 234 61 59 92 100 75 98 817 854 .428 2.335 2.935 2.642 2.241 1.982 52 264 2.107 .77 80 2030 7990 67 75 91 99 0 408 64 345 1.406 448 384 .711 1.768 .492 .822 .492
6 300 261 168 99 132 162 304 250 173 100 136 151 0 0 83 72 45 25 86 100 78 98 294 287 .815 1.227 1.11 1.206 1.042 2.053 52 292 1.114 .61 80 2180 7990 67 75 106 114 0 157 60 98 .739 151 91 1.353 .669 -.436 -.58 -.436
7 465 251 184 90 281 161 485 259 187 93 301 169 0 0 145 77 47 24 92 96 88 90 442 470 1.745 .573 .561 .513 .579 2.015 52 238 .442 .76 80 2330 7990 67 75 121 129 0 151 54 97 .345 156 102 2.897 .338 -1.535 -1.564 -1.535
8 1076 6530 190 93 886 6437 1021 6017 195 97 831 5924 0 0 465 3116 50 29 100 100 96 100 7323 6755 .138 7.265 7.129 7.612 7.385 1.58 52 287 7.422 .92 90 2460 7990 66 75 133 142 0 3934 56 3878 4.377 3625 3569 .228 4.294 2.13 2.102 2.13
9 906 1779 207 100 699 1679 964 1933 215 105 757 1833 0 0 260 465 52 37 96 100 96 100 2378 2590 .416 2.402 2.421 2.468 2.386 1.413 32 214 2.496 .9 70 2610 8000 68 75 149 156 0 1072 60 1011 1.447 1164 1104 .691 1.459 .533 .545 .533
10 376 292 212 103 164 189 377 283 215 106 165 180 0 0 98 103 50 32 86 98 76 84 353 345 .868 1.152 1.091 1.075 1.096 2.384 52 275 1.069 .65 80 2760 7990 67 75 164 172 0 176 62 114 .694 170 108 1.44 .657 -.526 -.606 -.526
11 704 886 214 102 490 784 703 813 216 105 489 711 0 0 238 336 51 25 96 100 94 100 1274 1200 .625 1.6 1.454 1.624 1.595 1.504 52 307 1.586 .92 90 2900 8000 67 76 177 186 0 534 61 472 .964 490 428 1.038 .876 -.053 -.191 -.053
12 777 1260 206 100 571 1160 726 1181 209 104 520 1081 0 0 305 515 49 26 98 100 96 100 1731 1601 .492 2.032 2.079 2.14 2.058 1.651 52 312 2.086 .87 90 3050 7990 66 75 192 201 0 759 60 699 1.224 711 651 .817 1.252 .291 .325 .291
13 613 863 212 106 401 757 655 902 214 110 443 796 0 0 194 359 53 30 92 100 90 100 1158 1239 .53 1.888 1.797 1.841 1.948 2.147 52 284 2.048 .85 80 3200 7990 67 75 208 216 0 520 64 456 1.137 543 480 .879 1.082 .186 .114 .186
14 447 337 223 104 224 233 457 344 223 109 234 240 0 0 142 91 49 30 84 100 81 100 457 474 .961 1.04 1.026 1.174 .935 2.729 32 206 .837 .7 70 3350 7990 67 74 223 230 0 203 63 140 .627 207 145 1.596 .618 -.674 -.695 -.674
15 2128 4868 218 110 1910 4758 2207 5179 220 110 1989 5069 0 0 730 1842 53 26 98 100 96 100 6668 7058 .401 2.491 2.549 2.566 2.484 1.558 52 320 2.596 .95 90 3490 7990 66 75 236 245 0 2933 66 2866 1.501 3120 3054 .666 1.535 .586 .618 .586
16 1092 2425 219 115 873 2310 1131 2532 227 120 912 2417 0 0 293 697 61 39 94 100 94 100 3183 3329 .378 2.646 2.65 2.575 2.5 1.262 52 340 2.689 .94 90 3630 7990 66 75 250 259 0 1461 69 1392 1.594 1525 1456 .627 1.597 .673 .675 .673
17 327 221 222 109 105 112 334 223 228 114 112 114 0 0 99 64 94 38 57 84 19 73 217 226 .938 1.067 1.018 .892 .928 3.202 52 286 .641 .6 80 3780 7990 67 75 266 274 0 133 66 67 .643 134 69 1.556 .613 -.638 -.706 -.638
18 379 217 216 105 163 112 391 212 219 108 175 107 0 0 108 64 47 28 87 84 84 84 275 282 1.455 .687 .611 .518 .633 2.615 32 214 .535 .61 70 3930 7990 67 74 281 288 0 131 63 67 .414 128 64 2.416 .368 -1.273 -1.441 -1.273
19 542 640 202 111 340 529 505 497 416 166 303 386 0 0 202 358 2832 482 0 48 0 17 869 689 .643 1.556 1.274 1.356 1.503 1.889 52 290 3.074 .54 80 4070 7990 67 75 295 303 0 386 67 319 .937 299 233 1.067 .767 -.093 -.382 -.093
20 383 244 206 106 177 138 394 255 212 109 188 149 0 0 116 74 46 30 90 93 81 81 315 337 1.283 .78 .793 .687 .761 2.092 32 170 .629 .63 60 4220 7990 68 74 311 317 0 147 64 83 .47 154 90 2.129 .477 -1.09 -1.067 -1.09

Total number of rows: 43008

Table truncated, full table size 9352 Kbytes.




Supplementary data files not provided
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