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Sample GSM91471 Query DataSets for GSM91471
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. fer-15 day 3 (5/30/00)
Sample type RNA
 
Channel 1
Source name fer-15 day 3 (5/30/00)
Organism Caenorhabditis elegans
Characteristics fer-15 day 3 (5/30/00)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name N2 ref. JL1
Organism Caenorhabditis elegans
Characteristics N2 ref. JL1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: aging, Aging
Image: http://smd.stanford.edu/MicroArray/gifs/2001-03/14308.gif
Measurement: time(absolute) 3 d
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jan 10, 2006
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) [email protected]
Phone 650-498-6012
URL http://genome-www5.stanford.edu/
Department Stanford University, School of Medicine
Street address 300 Pasteur Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2653
Series (1)
GSE4005 Aging time course

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 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
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

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
1 1264 968 70 168 1194 800 1257 991 87 182 1187 823 0 0 248 218 63 106 100 100 100 100 1994 2010 1.493 .67 .693 .659 .643 1.409 52 349 .635 .87 90 2730 19520 71 80 104 113 0 1352 235 1117 .936 1384 1149 1.069 .968 -.096 -.046
2 625 780 76 166 549 614 660 800 93 183 584 634 0 0 154 215 75 125 98 93 95 92 1163 1218 .894 1.118 1.086 1.068 1.119 1.716 80 461 1.182 .91 100 2900 19530 72 82 121 131 0 1089 232 858 1.562 1117 886 .64 1.516 .643 .601
3 276 288 71 156 205 132 290 262 74 163 219 106 0 0 96 75 18 45 100 93 96 71 337 325 1.553 .644 .484 .639 .615 2.063 32 171 .614 .53 60 3080 19540 75 81 141 147 0 402 218 184 .899 366 148 1.112 .676 -.153 -.565
4 1015 819 77 167 938 652 997 867 88 171 920 700 0 0 392 225 45 49 100 100 100 98 1590 1620 1.439 .695 .761 .706 .735 1.598 52 366 .62 .89 90 3220 19530 72 81 153 162 0 1144 233 911 .971 1211 978 1.03 1.063 -.043 .088
5 1839 361 69 163 1770 198 1074 357 100 167 1005 194 0 0 1720 179 151 45 93 75 78 59 1968 1199 8.939 .112 .193 .131 .111 1.942 32 230 .093 .83 70 3390 19520 72 79 171 178 0 504 228 277 .156 499 271 6.4 .27 -2.678 -1.891
6 118 180 64 159 54 21 79 160 66 160 15 1 0 0 83 79 15 45 46 28 37 18 75 16 2.571 .389 .067 1.358 1.321 2.953 32 236 1.504 .42 70 3540 19530 73 80 186 193 0 251 222 29 .543 223 1 1.841 .093 -.881 -3.425
7 1015 1222 68 168 947 1054 1061 1228 74 168 993 1060 0 0 319 425 42 46 98 98 97 98 2001 2053 .898 1.113 1.067 1.089 1.156 1.561 80 445 1.162 .93 100 3720 19540 73 83 203 213 0 1707 235 1472 1.555 1715 1481 .643 1.491 .636 .576
8 966 480 68 163 898 317 867 467 77 166 799 304 0 0 371 141 30 51 100 100 100 98 1215 1103 2.833 .353 .38 .348 .347 1.429 52 322 .32 .88 90 3870 19540 73 82 218 227 0 670 228 443 .493 652 425 2.028 .531 -1.02 -.912
9 8133 3303 122 200 8011 3103 8223 3282 236 216 8101 3082 0 0 1025 368 257 87 100 100 100 100 11114 11183 2.582 .387 .38 .388 .389 1.192 52 355 .371 .95 90 4030 19550 74 83 234 243 0 4613 279 4334 .541 4584 4305 1.848 .531 -.886 -.912
10 657 712 382 259 275 453 660 711 416 268 278 452 0 0 139 173 243 89 56 100 12 96 728 730 .607 1.647 1.626 1.757 1.769 1.687 32 176 1.576 .4 60 4190 19540 75 81 252 258 0 994 362 633 2.301 993 631 .435 2.271 1.202 1.183
11 3235 1823 73 172 3162 1651 3367 1860 170 226 3294 1688 0 0 767 405 382 363 100 100 100 98 4813 4982 1.915 .522 .512 .521 .517 1.274 52 361 .484 .93 90 4350 19550 74 83 266 275 0 2546 240 2306 .729 2598 2358 1.371 .716 -.455 -.482
12 445 564 67 156 378 408 445 561 73 166 378 405 0 0 108 131 37 48 100 100 100 100 786 783 .926 1.079 1.071 1.068 1.148 1.469 52 356 1.106 .85 90 4500 19550 74 83 281 290 0 788 218 570 1.508 784 566 .663 1.496 .592 .582
13 249 225 67 158 182 67 91 193 75 162 24 35 0 0 325 100 31 44 46 40 43 31 249 59 2.716 .368 1.458 .697 .734 3.952 32 228 .302 .68 70 4680 19550 75 82 300 307 0 314 221 94 .514 270 49 1.945 2.037 -.96 1.026
14 90 198 63 157 27 41 81 201 68 162 18 44 0 0 32 41 35 47 28 50 6 9 68 62 .659 1.519 2.444 2.135 1.714 3.272 32 226 1.089 .16 70 4820 19550 75 82 314 321 0 277 219 57 2.121 281 61 .471 3.414 1.085 1.772
15 116 208 68 162 48 46 78 197 78 165 10 35 0 0 96 79 50 46 21 43 9 18 94 45 1.043 .958 3.5 2.155 2.165 3.511 32 236 1.029 .57 70 4980 19550 75 82 330 337 0 291 226 64 1.339 275 49 .747 4.888 .421 2.289
16 491 458 66 164 425 294 478 440 78 166 412 276 0 0 203 134 48 49 100 96 100 94 719 688 1.446 .692 .67 .699 .724 1.751 52 293 .665 .82 80 5150 19570 77 85 347 355 0 640 229 411 .966 615 385 1.035 .936 -.05 -.096
17 814 530 65 162 749 368 382 447 67 165 317 285 0 0 856 325 17 45 100 90 100 78 1117 602 2.035 .491 .899 .517 .55 2.436 32 164 .377 .84 60 5310 19570 78 84 364 370 -100 740 226 514 .686 624 398 1.457 1.256 -.543 .329
18 553 458 70 167 483 291 573 441 75 173 503 274 0 0 138 111 29 52 100 100 100 100 774 777 1.66 .602 .545 .587 .59 1.561 52 364 .597 .82 90 5470 19560 75 84 378 387 0 640 233 406 .841 616 383 1.188 .761 -.249 -.394
19 522 692 67 171 455 521 565 675 77 173 498 504 0 0 282 335 51 49 98 100 88 92 976 1002 .873 1.145 1.012 1.174 1.265 1.86 52 312 1.211 .81 80 5640 19570 77 85 396 404 0 967 239 728 1.599 943 704 .625 1.414 .677 .499
20 1081 1021 66 169 1015 852 1266 1159 69 170 1200 990 0 0 549 487 23 49 100 98 100 96 1867 2190 1.191 .839 .825 .815 .886 1.841 80 368 .85 .89 100 5800 19570 76 86 411 421 0 1426 236 1190 1.172 1619 1383 .853 1.152 .229 .204

Total number of rows: 21504

Table truncated, full table size 4693 Kbytes.




Supplementary data files not provided
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