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Sample GSM39987 Query DataSets for GSM39987
Status Public on Feb 21, 2005
Title Pericardium 0465
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Pericardium 0465
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-04/16015.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
1 407 353 264 255 143 98 404 342 270 254 140 87 0 0 84 66 60 69 82 67 63 28 241 227 1.459 .685 .621 .821 .798 3.121 52 181 .801 .44 80 1090 9350 63 71 61 69 0 357 258 99 .692 345 88 1.445 .628 -.531 -.672 -.531
2 367 489 271 263 96 226 285 307 275 266 14 44 0 0 195 408 59 72 33 42 23 30 322 58 .425 2.354 3.143 1.758 2 3.216 80 328 2.264 .88 100 1200 9320 59 69 71 81 -50 494 266 228 2.378 310 44 .421 3.175 1.667 1.25
3 3501 2097 269 253 3232 1844 3450 2121 275 262 3181 1868 0 0 973 497 66 78 100 100 100 100 5076 5049 1.753 .571 .587 .575 .554 1.187 52 191 .549 .97 90 1370 9350 62 71 88 97 0 2118 256 1863 .576 2142 1887 1.735 .593 -.795 -.753 -.795
4 325 286 265 249 60 37 274 257 268 256 9 8 0 0 138 128 54 70 35 26 20 12 97 17 1.622 .617 .889 1.096 1.183 4.001 80 297 .965 .61 100 1480 9320 59 69 99 109 -50 289 252 37 .623 260 8 1.605 .898 -.155 -.683
5 1005 2956 265 237 740 2719 995 3135 268 252 730 2898 0 0 283 647 59 80 97 100 97 100 3459 3628 .272 3.674 3.97 3.748 3.895 1.329 80 218 3.969 .95 100 1650 9340 61 71 116 126 0 2986 239 2746 3.711 3167 2927 .269 4.01 1.892 2.004 1.892
6 365 372 269 254 96 118 307 305 273 261 38 51 0 0 165 203 59 70 42 45 26 27 214 89 .814 1.229 1.342 1.207 1.205 3.066 80 275 1.4 .8 100 1750 9320 59 69 126 136 -50 376 257 119 1.242 308 52 .805 1.356 .439 .312
7 844 1105 273 267 571 838 858 1120 292 310 585 853 0 0 167 204 146 241 98 98 93 96 1409 1438 .681 1.468 1.458 1.499 1.429 1.449 80 217 1.492 .91 100 1920 9350 62 72 143 153 0 1116 270 846 1.482 1131 862 .675 1.473 .568 .559 .568
8 717 1049 270 270 447 779 607 1074 374 429 337 804 0 0 476 748 315 443 51 57 46 48 1226 1141 .574 1.743 2.386 1.818 1.637 2.536 80 258 1.644 .94 100 2020 9320 59 69 153 163 -50 1060 273 787 1.76 1085 812 .568 2.41 1.269 .816
9 431 503 273 285 158 218 376 321 358 407 103 36 0 0 200 415 283 398 20 20 6 11 376 139 .725 1.38 .35 1.306 1.213 3.127 80 304 1.776 .89 100 2160 9320 59 69 167 177 -50 508 288 220 1.394 324 36 .718 .353 -1.502 .479
10 446 384 277 272 169 112 451 379 283 281 174 107 0 0 72 99 56 73 92 61 78 28 281 281 1.509 .663 .615 .751 .697 2.087 52 228 .875 .45 90 2320 9330 60 69 183 192 0 388 275 113 .669 383 108 1.494 .621 -.579 -.687 -.579
11 1760 447 294 298 1466 149 1714 442 302 304 1420 144 0 0 495 115 62 82 100 68 100 41 1615 1564 9.839 .102 .101 .091 .09 2.059 80 265 .098 .62 100 2450 9330 60 70 196 206 0 452 301 151 .103 446 145 9.741 .102 -3.284 -3.287 -3.284
12 745 1169 293 311 452 858 701 1106 306 312 408 795 0 0 180 458 67 84 100 100 100 100 1310 1203 .527 1.898 1.949 1.72 1.933 1.564 32 171 2.175 .86 70 2580 9300 58 65 210 217 0 1181 314 867 1.917 1117 803 .522 1.968 .939 .977 .939
13 684 615 297 288 387 327 677 593 302 297 380 305 0 0 108 126 60 87 100 96 100 87 714 685 1.183 .845 .803 .795 .825 1.719 32 166 .95 .77 70 2720 9330 61 68 224 231 0 621 291 330 .853 599 308 1.172 .811 -.229 -.303 -.229
14 739 693 293 273 446 420 733 697 296 282 440 424 0 0 122 147 55 75 100 96 100 94 866 864 1.062 .942 .964 .889 .885 1.551 52 262 .96 .87 90 2840 9320 59 68 235 244 0 700 276 424 .951 704 428 1.051 .973 -.072 -.039 -.072
15 747 727 288 272 459 455 741 705 291 282 453 433 0 0 172 147 62 75 100 100 100 100 914 886 1.009 .991 .956 1.009 1.026 1.328 32 178 .956 .88 70 2980 9310 59 66 250 257 0 734 275 460 1.001 712 437 .999 .966 .002 -.051 .002
16 2134 1661 285 256 1849 1405 2215 1731 323 334 1930 1475 0 0 400 304 458 891 100 91 96 6 3254 3405 1.316 .76 .764 .761 .796 1.271 80 307 .75 .96 100 3120 9310 58 68 263 273 0 1678 259 1419 .768 1748 1490 1.303 .772 -.382 -.373 -.382
17 950 1126 281 268 669 858 944 1128 338 375 663 860 0 0 171 248 552 1074 76 21 0 0 1527 1523 .78 1.283 1.297 1.266 1.243 1.369 52 210 1.344 .9 90 3240 9310 58 67 275 284 0 1137 271 867 1.295 1139 869 .772 1.31 .373 .39 .373
18 638 376 293 288 345 88 650 365 298 293 357 77 0 0 104 83 64 81 100 48 97 17 433 434 3.92 .255 .216 .246 .258 2.426 80 238 .264 .43 100 3370 9330 60 70 288 298 0 380 291 89 .258 369 78 3.881 .218 -1.957 -2.198 -1.957
19 514 467 293 278 221 189 505 451 294 288 212 173 0 0 77 93 64 72 98 94 90 61 410 385 1.169 .855 .816 .8 .822 1.898 52 212 .879 .58 90 3500 9330 60 69 301 310 0 472 281 191 .864 456 175 1.158 .824 -.211 -.279 -.211
20 1745 2349 294 303 1451 2046 1718 2366 293 309 1424 2063 0 0 438 570 58 75 100 100 100 100 3497 3487 .709 1.41 1.449 1.416 1.388 1.178 80 267 1.399 .97 100 3650 9330 60 70 316 326 0 2373 306 2067 1.424 2390 2084 .702 1.463 .51 .549 .51

Total number of rows: 44160

Table truncated, full table size 9581 Kbytes.




Supplementary data files not provided
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