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Sample GSM39917 Query DataSets for GSM39917
Status Public on Feb 21, 2005
Title Ovary 0314
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Ovary 0314
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/26560.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
1 296 655 138 65 158 590 286 707 145 66 148 642 0 0 77 213 50 13 90 100 82 100 748 790 .268 3.734 4.338 3.985 4.355 2.065 52 288 4.078 .7 80 1310 7840 32 40 35 43 0 668 66 602 3.81 721 655 .262 4.426 1.93 2.146 1.93
2 277 95 141 64 136 31 278 95 148 67 137 31 0 0 56 18 49 14 96 82 76 53 167 168 4.387 .228 .226 .206 .264 2.538 52 256 .145 .52 80 1460 7840 32 40 50 58 0 97 65 32 .233 97 32 4.299 .231 -2.104 -2.115 -2.104
3 725 597 134 67 591 530 786 622 136 68 652 555 0 0 231 183 30 11 98 100 98 100 1121 1207 1.115 .897 .851 .975 .969 2.105 52 312 .848 .86 90 1600 7840 31 40 63 72 0 609 68 541 .915 635 566 1.093 .869 -.128 -.203 -.128
4 2154 4811 132 67 2022 4744 2261 5283 139 72 2129 5216 0 0 1099 2205 82 91 100 100 98 100 6766 7345 .426 2.346 2.45 2.545 2.343 1.893 52 331 2.32 .89 90 1750 7830 30 39 78 87 0 4909 68 4841 2.394 5391 5322 .418 2.5 1.259 1.322 1.259
5 395 183 137 67 258 116 414 197 145 75 277 130 0 0 97 45 99 113 87 65 87 0 374 407 2.224 .45 .469 .454 .478 2.906 32 214 .39 .77 70 1890 7850 33 40 93 100 0 187 68 118 .459 201 133 2.18 .479 -1.124 -1.062 -1.124
6 270 110 136 69 134 41 277 112 138 69 141 43 0 0 59 21 29 11 92 90 88 76 175 184 3.268 .306 .305 .306 .276 3.196 52 277 .218 .6 80 2040 7840 32 40 108 116 0 112 70 42 .312 114 44 3.203 .311 -1.679 -1.684 -1.679
7 524 151 134 68 390 83 562 157 138 70 428 89 0 0 140 29 28 12 100 96 98 96 473 517 4.699 .213 .208 .217 .227 1.987 52 282 .175 .79 90 2190 7840 31 40 122 131 0 154 69 85 .217 160 91 4.605 .212 -2.203 -2.237 -2.203
8 1214 4075 132 70 1082 4005 1229 3873 136 70 1097 3803 0 0 643 2613 30 11 98 100 98 100 5087 4900 .27 3.701 3.467 3.48 3.714 2.624 80 352 4.373 .86 100 2340 7840 31 41 137 147 0 4158 71 4087 3.777 3952 3881 .265 3.537 1.917 1.823 1.917
9 448 384 136 67 312 317 482 414 139 68 346 347 0 0 129 101 30 12 96 100 96 100 629 693 .984 1.016 1.003 1.035 .989 1.687 52 254 .961 .86 80 2480 7840 32 40 152 160 0 392 68 323 1.037 422 354 .965 1.023 .052 .033 .052
10 280 112 137 67 143 45 281 112 140 68 144 45 0 0 61 12 29 12 100 100 93 93 188 189 3.178 .315 .313 .337 .317 1.711 32 213 .227 .62 70 2630 7840 32 39 167 174 0 114 68 46 .321 114 46 3.114 .319 -1.639 -1.649 -1.639
11 566 526 136 69 430 457 581 550 139 70 445 481 0 0 200 171 33 11 96 100 96 100 887 926 .941 1.063 1.081 1.174 1.168 1.95 52 278 1.011 .85 80 2770 7840 32 40 181 189 0 537 70 466 1.084 561 491 .922 1.103 .117 .141 .117
12 690 707 131 71 559 636 688 754 136 71 557 683 0 0 187 202 30 11 96 100 94 100 1195 1240 .879 1.138 1.226 1.3 1.215 2.204 52 312 1.151 .92 90 2920 7840 31 40 195 204 0 721 72 649 1.161 769 697 .861 1.251 .215 .323 .215
13 392 341 133 72 259 269 397 362 138 72 264 290 0 0 96 81 30 12 96 100 96 100 528 554 .963 1.039 1.098 1.082 .972 1.512 52 234 .997 .88 80 3060 7840 32 40 210 218 0 348 73 274 1.06 369 296 .944 1.121 .084 .165 .084
14 280 122 132 74 148 48 279 124 138 74 147 50 0 0 68 22 31 11 92 92 90 86 196 197 3.083 .324 .34 .312 .316 2.505 52 256 .23 .61 80 3210 7840 32 40 225 233 0 124 76 49 .331 127 51 3.022 .347 -1.595 -1.527 -1.595
15 2246 3894 137 74 2109 3820 2486 4170 139 76 2349 4096 0 0 940 1434 29 13 100 100 96 100 5929 6445 .552 1.811 1.744 2.18 1.86 2 52 333 1.715 .95 90 3350 7830 30 39 238 247 0 3973 76 3898 1.848 4255 4180 .541 1.779 .886 .831 .886
16 830 1252 139 76 691 1176 868 1300 142 77 729 1224 0 0 208 378 31 13 96 100 96 100 1867 1953 .588 1.702 1.679 1.646 1.704 1.448 52 316 1.765 .93 90 3500 7840 31 40 253 262 0 1278 78 1200 1.737 1327 1249 .576 1.713 .796 .777 .796
17 236 112 143 77 93 35 232 111 144 78 89 34 0 0 58 19 30 13 90 88 75 71 128 123 2.657 .376 .382 .34 .375 2.33 52 274 .204 .51 80 3640 7840 32 40 268 276 0 114 79 36 .384 113 35 2.604 .39 -1.381 -1.359 -1.381
18 260 86 144 79 116 7 271 85 146 80 127 6 0 0 65 13 30 13 87 40 84 6 123 133 16.571 .06 .047 .14 .127 2.171 32 224 .024 .11 70 3790 7840 32 39 283 290 0 88 81 7 .062 87 6 16.24 .048 -4.021 -4.375 -4.021
19 356 322 144 80 212 242 364 335 151 81 220 255 0 0 104 118 64 14 94 96 80 96 454 475 .876 1.142 1.159 1.13 1.152 2.893 52 307 .947 .68 80 3940 7840 32 40 298 306 0 329 82 247 1.165 342 260 .859 1.183 .22 .242 .22
20 249 102 151 81 98 21 255 103 153 82 104 22 0 0 59 11 30 14 84 71 75 28 119 126 4.667 .214 .212 .196 .201 2.852 32 151 .145 .52 60 4090 7850 34 40 314 320 0 104 83 21 .219 105 22 4.573 .216 -2.193 -2.212 -2.193

Total number of rows: 43008

Table truncated, full table size 9035 Kbytes.




Supplementary data files not provided
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