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Sample GSM39981 Query DataSets for GSM39981
Status Public on Feb 21, 2005
Title Ovary 0466
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Ovary 0466
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-04/16012.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 GPL1825
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
1 285 217 177 211 108 6 291 206 179 214 114 -5 0 0 62 64 37 60 88 21 70 7 114 109 18 .056 null .491 .591 3.114 80 386 .622 .22 100 840 9870 90 100 59 69 0 231 224 6 .059 219 null 16.92 null -4.081 null -4.081
2 443 706 182 208 261 498 439 730 187 212 257 522 0 0 103 167 41 51 100 100 100 100 759 779 .524 1.908 2.031 1.92 2.083 1.531 12 90 2.587 .78 50 1000 9830 88 93 77 82 0 751 221 530 2.03 777 555 .493 2.161 1.021 1.112 1.021
3 2136 1062 174 209 1962 853 2237 1070 179 213 2063 861 0 0 786 345 40 60 100 100 100 98 2815 2924 2.3 .435 .417 .435 .422 1.334 80 281 .432 .96 100 1130 9850 88 98 88 98 0 1130 222 907 .463 1138 916 2.162 .444 -1.112 -1.171 -1.112
4 483 505 165 230 318 275 434 460 169 229 269 230 0 0 217 257 37 63 96 71 93 65 593 499 1.156 .865 .855 .732 .83 2.741 32 100 .995 .81 60 1270 9850 90 96 104 110 0 537 245 293 .92 489 245 1.087 .91 -.12 -.137 -.12
5 687 3131 170 230 517 2901 620 2987 175 235 450 2757 0 0 230 735 40 67 100 100 98 100 3418 3207 .178 5.611 6.127 5.939 6.294 1.483 80 208 6.795 .91 100 1400 9850 88 98 115 125 0 3331 245 3086 5.969 3178 2933 .168 6.518 2.578 2.704 2.578
6 180 231 165 210 15 21 175 220 173 223 10 10 0 0 57 75 48 72 17 22 7 5 36 20 .714 1.4 1 1.22 1.375 3.835 80 294 1.593 .53 100 1510 9810 84 94 126 136 -50 246 223 22 1.489 234 11 .671 1.064 .089 .575
7 460 378 162 215 298 163 459 362 172 228 297 147 0 0 100 105 52 71 98 80 97 51 461 444 1.828 .547 .495 .484 .522 1.929 80 239 .594 .73 100 1680 9850 88 98 143 153 0 402 229 173 .582 385 156 1.719 .527 -.781 -.925 -.781
8 705 1053 165 217 540 836 689 990 172 228 524 773 0 0 175 345 46 76 98 100 98 98 1376 1297 .646 1.548 1.475 1.541 1.525 1.459 80 163 1.596 .91 100 1810 9850 88 98 156 166 0 1120 231 889 1.647 1053 822 .607 1.569 .72 .65 .72
9 278 244 169 216 109 28 236 220 172 223 67 4 0 0 158 111 39 64 60 26 46 11 137 71 3.893 .257 .06 .524 .715 3.964 80 285 .6 .39 100 1920 9810 84 94 167 177 -50 260 230 30 .273 234 4 3.659 .064 -3.977 -1.872
10 371 1503 174 212 197 1291 328 1442 174 222 154 1230 0 0 126 424 37 65 93 100 91 98 1488 1384 .153 6.553 7.987 7.893 7.429 1.809 80 255 6.111 .86 100 2080 9830 86 96 183 193 0 1599 226 1373 6.972 1534 1309 .143 8.497 2.801 3.087 2.801
11 1888 377 173 230 1715 147 1809 335 174 238 1636 105 0 0 580 158 40 74 100 65 100 38 1862 1741 11.667 .086 .064 .083 .093 2.134 80 231 .099 .65 100 2210 9820 85 95 196 206 0 401 245 156 .091 356 112 10.967 .068 -3.455 -3.872 -3.455
12 637 756 165 233 472 523 590 708 170 237 425 475 0 0 242 313 41 65 100 98 98 92 995 900 .902 1.108 1.118 1.063 1.09 1.668 52 190 1.213 .89 80 2330 9810 85 93 209 217 -100 804 248 556 1.179 753 505 .848 1.189 .25 .237
13 594 611 168 225 426 386 545 500 174 232 377 275 0 0 209 302 42 64 100 100 100 86 812 652 1.104 .906 .729 .77 .815 1.648 52 202 1.119 .85 80 2480 9810 85 93 224 232 0 650 239 411 .964 532 293 1.037 .776 -.053 -.366 -.053
14 703 689 174 225 529 464 670 626 177 229 496 401 0 0 176 222 37 64 100 98 100 94 993 897 1.14 .877 .808 .803 .876 1.669 52 251 .958 .9 90 2600 9810 84 93 235 244 0 733 239 494 .933 666 427 1.072 .86 -.1 -.217 -.1
15 1042 1416 174 219 868 1197 1047 1357 179 221 873 1138 0 0 225 307 38 61 100 100 100 100 2065 2011 .725 1.379 1.304 1.375 1.483 1.23 32 169 1.402 .94 70 2740 9790 83 90 250 257 0 1506 233 1273 1.467 1444 1211 .682 1.387 .553 .472 .553
16 1758 1474 171 210 1587 1264 1714 1450 176 218 1543 1240 0 0 312 269 41 67 100 100 100 100 2851 2783 1.256 .796 .804 .795 .789 1.209 80 256 .795 .96 100 2870 9810 84 94 262 272 0 1568 223 1345 .847 1543 1319 1.18 .855 -.239 -.226 -.239
17 611 847 172 212 439 635 589 801 175 217 417 589 0 0 198 292 38 61 100 100 96 98 1074 1006 .691 1.446 1.412 1.457 1.498 1.487 80 241 1.496 .91 100 2990 9810 84 94 274 284 0 901 226 676 1.539 852 627 .65 1.503 .622 .587 .622
18 431 238 171 221 260 17 433 236 174 228 262 15 0 0 67 62 42 66 100 17 100 1 277 277 15.294 .065 .057 .135 .155 2.67 52 208 -1 -1 90 3120 9810 84 93 287 296 0 253 235 18 .07 251 16 14.376 .061 -3.846 -4.037 -3.846
19 461 1331 178 219 283 1112 443 1382 235 257 265 1163 0 0 135 499 380 274 23 88 1 86 1395 1428 .254 3.929 4.389 3.625 4.709 2.717 80 264 2.387 .48 100 3260 9820 85 95 301 311 0 1416 233 1183 4.18 1470 1237 .239 4.669 2.064 2.223 2.064
20 1419 1885 177 225 1242 1660 1410 1863 226 258 1233 1638 0 0 848 1275 353 254 76 78 63 75 2902 2871 .748 1.337 1.328 1.218 1.338 2.151 80 307 1.296 .87 110 3410 9810 83 94 315 326 -100 2005 239 1766 1.422 1982 1743 .703 1.413 .499 .508

Total number of rows: 44160

Table truncated, full table size 9593 Kbytes.




Supplementary data files not provided
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