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Sample GSM39923 Query DataSets for GSM39923
Status Public on Feb 21, 2005
Title Cervix 2209
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Cervix 2209
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-12/35854.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
1 456 393 140 346 316 47 474 393 161 349 334 47 0 0 164 216 69 94 87 46 87 25 363 381 6.723 .149 .141 .414 .476 3.754 32 148 .507 .13 60 1710 8280 65 71 64 70 0 468 412 56 .177 468 56 5.648 .168 -2.498 -2.578 -2.498
2 379 263 140 318 239 -55 429 313 155 327 289 -5 0 0 150 148 62 88 78 13 76 5 184 284 null null null .321 .23 4.816 52 260 11.375 .04 80 1870 8280 64 72 79 87 -50 313 379 -65 null 373 null null null null null
3 940 1070 153 322 787 748 1053 1113 168 341 900 791 0 0 332 321 77 124 98 96 93 91 1535 1691 1.052 .95 .879 .95 .979 2.241 80 328 .923 .79 100 2010 8280 63 73 92 102 0 1274 383 890 1.131 1325 942 .884 1.046 .178 .065 .178
4 2242 2060 155 319 2087 1741 2060 2042 165 335 1905 1723 0 0 1528 1269 69 119 93 90 88 82 3828 3628 1.199 .834 .904 .897 .711 4.819 80 343 .773 .73 100 2150 8280 63 73 106 116 0 2452 380 2073 .993 2431 2051 1.007 1.077 -.01 .107 -.01
5 363 1759 161 307 202 1452 386 1742 175 315 225 1435 0 0 175 894 77 95 73 90 57 84 1654 1660 .139 7.188 6.378 5.947 6.854 1.901 52 321 6.958 .73 90 2300 8290 64 73 121 130 0 2094 365 1729 8.557 2074 1708 .117 7.593 3.097 2.925 3.097
6 419 433 166 329 253 104 430 469 183 328 264 140 0 0 131 172 85 93 87 62 78 34 357 404 2.433 .411 .53 .749 .717 2.282 32 153 .991 .44 60 2430 8290 66 72 136 142 0 515 392 124 .489 558 167 2.043 .631 -1.031 -.664 -1.031
7 374 11749 152 272 222 11477 397 12875 165 288 245 12603 0 0 167 5717 72 103 76 100 66 100 11699 12848 .019 51.698 51.441 36.845 41.002 1.758 80 383 59.714 .7 100 2590 8290 64 74 150 160 0 13987 324 13663 61.545 15327 15004 .016 61.239 5.944 5.936 5.944
8 2635 3244 147 266 2488 2978 2918 3541 158 280 2771 3275 0 0 1286 1359 59 106 100 98 100 98 5466 6046 .835 1.197 1.182 1.236 1.167 2.617 80 388 1.195 .76 100 2750 8280 63 73 166 176 0 3862 317 3545 1.425 4215 3899 .702 1.407 .511 .493 .511
9 448 844 147 280 301 564 430 854 155 284 283 574 0 0 231 456 58 96 80 84 73 76 865 857 .534 1.874 2.028 2.166 1.791 2.53 52 230 2.149 .78 80 2880 8280 64 72 180 188 0 1005 333 671 2.231 1017 683 .448 2.415 1.157 1.272 1.157
10 276 316 143 263 133 53 265 289 148 273 122 26 0 0 142 138 57 84 67 30 51 19 186 148 2.509 .398 .213 .636 .714 3.624 52 266 1.012 .43 80 3030 8270 63 71 195 203 -50 376 313 63 .474 344 31 2.108 .254 -1.979 -1.076
11 913 659 147 274 766 385 897 689 153 279 750 415 0 0 213 189 51 83 100 94 100 86 1151 1165 1.99 .503 .553 .427 .534 2.19 52 310 .488 .76 90 3180 8270 62 71 209 218 0 785 326 458 .598 820 494 1.671 .659 -.741 -.602 -.741
12 584 629 141 317 443 312 564 580 165 320 423 263 0 0 317 303 88 90 81 81 81 71 755 686 1.42 .704 .622 .957 .91 2.703 32 210 .842 .62 70 3310 8270 63 70 223 230 0 749 377 371 .838 690 313 1.193 .74 -.254 -.434 -.254
13 506 561 147 283 359 278 510 561 164 294 363 278 0 0 223 235 65 96 87 75 84 62 637 641 1.291 .774 .766 .719 .81 2.554 32 226 .692 .5 70 3460 8270 63 70 238 245 0 668 337 331 .922 668 331 1.085 .912 -.117 -.133 -.117
14 403 297 146 251 257 46 402 301 159 257 256 50 0 0 130 89 112 86 84 31 59 6 303 306 5.587 .179 .195 .264 .349 2.727 32 204 .194 .23 70 3620 8290 65 72 254 261 0 354 299 55 .213 358 60 4.693 .233 -2.231 -2.105 -2.231
15 1995 1774 144 242 1851 1532 2018 1886 153 249 1874 1644 0 0 1070 747 97 85 92 96 90 94 3383 3518 1.208 .828 .877 .84 .806 2.343 52 305 .748 .85 90 3760 8280 63 72 267 276 0 2112 288 1824 .985 2245 1957 1.015 1.044 -.021 .063 -.021
16 1205 1126 148 237 1057 889 1330 1250 151 244 1182 1013 0 0 524 494 51 75 98 94 96 92 1946 2195 1.189 .841 .857 .81 .87 3.125 52 317 .789 .78 90 3900 8270 62 71 281 290 0 1340 282 1058 1.001 1488 1206 .999 1.02 .002 .029 .002
17 344 236 152 239 192 -3 351 210 166 245 199 -29 0 0 120 100 73 83 87 21 65 6 189 170 null null null .505 .367 5.458 32 218 .122 .09 70 4040 8260 62 69 296 303 0 281 285 -4 null 250 null null null null null null
18 359 261 145 236 214 25 371 239 155 245 226 3 0 0 158 117 55 76 78 28 75 15 239 229 8.56 .117 .013 .357 .552 4.425 32 170 .102 .08 60 4200 8270 64 70 313 319 0 311 281 30 .139 285 4 7.19 .016 -2.846 -5.984 -2.846
19 542 404 138 244 404 160 530 433 145 255 392 189 0 0 161 162 50 87 100 70 100 51 564 581 2.525 .396 .482 .47 .518 2.137 80 468 .411 .45 110 4360 8270 61 72 326 337 0 481 290 190 .471 515 225 2.121 .574 -1.085 -.801 -1.085
20 310 282 138 255 172 27 317 274 146 266 179 19 0 0 132 123 50 89 75 34 65 13 199 198 6.37 .157 .106 .383 .504 4.373 52 212 .518 .18 80 4490 8270 63 71 341 349 -50 336 304 32 .187 326 23 5.351 .126 -2.984 -2.42

Total number of rows: 43008

Table truncated, full table size 9277 Kbytes.




Supplementary data files not provided
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