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Sample GSM39968 Query DataSets for GSM39968
Status Public on Feb 21, 2005
Title Liver 0586
Sample type RNA
 
Channel 1
Source name Cy3 - CRG
Organism Homo sapiens
Extracted molecule total RNA
 
Channel 2
Source name Cy5 - Liver 0586
Organism Homo sapiens
Extracted molecule total RNA
 
 
Description Simple annotation: Normal tissue, Normal tissue
Image: http://jdemeter-smd.stanford.edu:8000/MicroArray/gifs/2001-04/15157.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
1 676 104 587 186 89 -82 674 81 601 192 87 -105 0 0 74 71 117 88 33 3 2 2 7 -18 null null null 1.469 1.309 3.743 80 376 1.431 .23 100 870 8050 52 62 46 56 -100 114 204 -90 null 89 null null null null null
2 569 210 578 213 -9 -3 551 207 602 257 -27 -6 0 0 87 56 123 184 7 0 1 0 -12 -33 null null null .666 .608 4.789 80 280 2.085 .63 100 1000 8050 52 62 59 69 -100 231 234 -3 null 227 null null null null null
3 1510 575 524 227 986 348 690 264 672 306 166 37 0 0 1178 473 523 261 41 40 38 35 1334 203 2.833 .353 .223 .443 .398 2.498 80 255 .381 .9 100 1140 8050 52 62 73 83 -100 632 249 382 .388 290 41 2.578 .245 -2.03 -1.366
4 512 210 469 226 43 -16 508 197 633 282 39 -29 0 0 80 53 546 214 0 0 0 0 27 10 null null null .981 .835 4.105 80 242 .399 .93 100 1270 8050 52 62 86 96 -100 231 248 -18 null 216 null null null null null
5 878 440 458 220 420 220 539 296 528 251 81 76 0 0 552 253 254 144 45 46 40 37 640 157 1.909 .524 .938 .598 .508 2.556 80 228 .472 .9 100 1410 8050 52 62 100 110 -100 484 242 242 .576 325 84 1.737 1.031 .044 -.797
6 482 211 464 224 18 -13 482 206 532 249 18 -18 0 0 73 49 247 133 0 1 0 0 5 0 null null null .873 .8 3.821 80 233 .452 .82 100 1550 8040 51 61 114 124 -100 232 246 -14 null 226 null null null null null
7 682 299 463 224 219 75 516 243 528 257 53 19 0 0 329 140 197 134 32 30 30 13 294 72 2.92 .342 .358 .378 .359 3.24 80 248 .418 .69 100 1680 8040 51 61 127 137 -100 329 246 82 .376 267 21 2.657 .394 -1.344 -1.41
8 748 315 445 229 303 86 497 241 544 275 52 12 0 0 434 163 240 150 36 32 32 17 389 64 3.523 .284 .231 .479 .409 3.072 80 249 .365 .84 100 1820 8040 51 61 141 151 -100 346 252 95 .312 265 13 3.206 .254 -1.979 -1.681
9 602 279 404 214 198 65 483 230 450 234 79 16 0 0 284 132 174 91 30 31 17 17 263 95 3.046 .328 .203 .631 .535 2.695 80 300 .419 .8 100 1950 8040 51 61 154 164 -100 307 235 71 .361 253 18 2.772 .223 -2.168 -1.471
10 673 366 421 215 252 151 681 364 428 219 260 149 0 0 99 83 70 54 96 90 86 69 403 409 1.669 .599 .573 .53 .592 2.19 52 210 .534 .61 80 2120 8040 52 60 172 180 -100 402 236 166 .658 400 164 1.519 .63 -.667 -.603
11 2143 662 459 213 1684 449 2220 659 471 218 1761 446 0 0 365 138 63 59 100 100 100 100 2133 2207 3.751 .267 .253 .259 .257 1.285 52 215 .262 .93 90 2250 8040 51 60 184 193 -100 727 234 493 .293 724 490 3.413 .278 -1.845 -1.771
12 1073 692 480 223 593 469 1108 703 490 223 628 480 0 0 137 109 77 55 100 100 100 100 1062 1108 1.264 .791 .764 .791 .835 1.245 32 150 .79 .89 70 2360 8050 53 60 196 203 -100 760 245 515 .869 773 527 1.151 .84 -.252 -.202
13 925 515 530 214 395 301 931 504 531 219 401 290 0 0 164 127 77 53 98 100 88 96 696 691 1.312 .762 .723 .779 .762 1.567 52 253 .702 .8 90 2510 8050 52 61 210 219 -100 566 235 331 .837 554 319 1.194 .795 -.331 -.256
14 1063 788 511 209 552 579 1059 784 520 217 548 575 0 0 161 168 76 54 100 100 100 100 1131 1123 .953 1.049 1.049 1.052 1.021 1.449 52 213 1.058 .88 80 2640 8040 52 60 224 232 -100 866 230 636 1.153 862 632 .868 1.153 .205 .205
15 1188 863 505 218 683 645 1184 876 510 221 679 658 0 0 180 201 69 55 100 100 100 100 1328 1337 1.059 .944 .969 .925 .946 1.353 32 158 .992 .91 70 2780 8040 52 59 238 245 -100 948 240 709 1.038 963 723 .964 1.065 .091 .053
16 1525 1017 510 228 1015 789 1585 1017 517 229 1075 789 0 0 291 202 84 55 100 100 100 100 1804 1864 1.286 .777 .734 .787 .778 1.297 80 325 .764 .94 100 2900 8050 52 62 249 259 -100 1118 251 867 .854 1118 867 1.171 .807 -.31 -.227
17 990 472 492 233 498 239 1020 459 507 231 528 226 0 0 134 110 114 64 100 96 96 87 737 754 2.084 .48 .428 .448 .435 1.702 32 140 .495 .69 60 3030 8040 53 59 264 270 -100 519 256 263 .527 504 248 1.896 .47 -1.088 -.923
18 700 306 456 219 244 87 672 298 488 223 216 79 0 0 230 151 131 84 65 46 40 28 331 295 2.805 .357 .366 .484 .612 1.971 32 141 .614 .56 60 3160 8040 53 59 277 283 -100 336 241 96 .392 327 87 2.552 .402 -1.315 -1.352
19 669 421 378 213 291 208 656 412 398 216 278 199 0 0 94 81 96 70 100 93 85 78 499 477 1.399 .715 .716 .689 .636 1.6 80 294 .657 .73 100 3300 8050 52 62 289 299 -100 463 234 229 .785 453 219 1.273 .787 -.346 -.348
20 1180 1007 359 216 821 791 1200 1072 362 220 841 856 0 0 190 232 51 54 100 100 100 100 1612 1697 1.038 .963 1.018 .944 .965 1.267 52 220 .97 .95 90 3440 8040 51 60 303 312 -100 1107 237 869 1.059 1178 941 .945 1.119 .162 .082

Total number of rows: 44160

Table truncated, full table size 9794 Kbytes.




Supplementary data files not provided
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