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Sample GSM91449 Query DataSets for GSM91449
Status Public on Jan 11, 2006
Title N2 ref. JL1 vs. fer-15 day 3 (8/6/00)
Sample type RNA
 
Channel 1
Source name fer-15 day 3 (8/6/00)
Organism Caenorhabditis elegans
Characteristics fer-15 day 3 (8/6/00)
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, adult
Image: http://smd.stanford.edu/MicroArray/gifs/2001-02/13708.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
1 826 2154 235 98 591 2056 886 2616 241 115 651 2518 0 0 352 1176 63 74 96 100 90 93 2647 3169 .287 3.479 3.868 3.232 3.547 1.677 32 220 3.55 .95 70 1800 19100 70 77 112 119 0 2636 120 2516 4.257 3201 3082 .235 4.734 2.09 2.243
2 1417 2086 240 76 1177 2010 1401 2085 263 118 1161 2009 0 0 225 137 122 210 100 100 100 100 3187 3170 .586 1.708 1.73 1.735 1.731 1.233 32 218 1.838 .94 70 1950 19100 70 77 127 134 0 2553 93 2460 2.09 2552 2459 .478 2.118 1.063 1.082
3 843 242 243 47 600 195 829 224 292 53 586 177 0 0 148 67 303 31 100 100 41 100 795 763 3.077 .325 .302 .317 .278 1.335 12 72 .17 .77 50 2120 19080 69 74 145 150 0 296 58 239 .398 274 217 2.514 .37 -1.33 -1.436
4 756 1396 233 45 523 1351 798 1469 237 46 565 1424 0 0 247 669 56 11 96 100 90 100 1874 1989 .387 2.583 2.52 2.501 2.752 1.953 32 206 2.837 .89 70 2260 19090 69 76 158 165 0 1708 55 1653 3.161 1798 1743 .316 3.084 1.661 1.625
5 1623 1574 238 46 1385 1528 1713 1636 247 53 1475 1590 0 0 983 1056 66 25 93 100 81 100 2913 3065 .906 1.103 1.078 1.213 1.161 1.666 32 193 1.1 .94 70 2430 19080 68 75 175 182 0 1926 56 1870 1.35 2002 1946 .741 1.319 .433 .4
6 279 54 230 45 49 9 268 49 237 50 38 4 0 0 107 15 59 22 37 18 18 3 58 42 5.444 .184 .105 .196 .246 3.247 32 220 .049 .33 70 2580 19090 69 76 190 197 0 66 55 11 .225 60 5 4.449 .129 -2.153 -2.957
7 2168 4837 240 55 1928 4782 1968 4464 245 77 1728 4409 0 0 798 1215 74 105 100 100 100 100 6710 6137 .403 2.48 2.552 2.624 2.657 1.336 32 220 2.459 .93 70 2750 19090 69 76 207 214 0 5920 67 5852 3.035 5463 5396 .329 3.123 1.602 1.643
8 531 134 237 48 294 86 525 132 241 57 288 84 0 0 144 49 54 28 90 87 90 71 380 372 3.419 .293 .292 .31 .277 1.94 32 220 .218 .73 70 2910 19090 69 76 223 230 0 164 59 105 .358 162 103 2.793 .357 -1.482 -1.486
9 8045 6820 299 95 7746 6725 8081 6715 400 230 7782 6620 0 0 1109 379 439 463 100 100 100 100 14471 14402 1.152 .868 .851 .876 .841 1.187 32 220 .858 .92 70 3080 19090 69 76 240 247 0 8346 116 8230 1.063 8218 8102 .941 1.041 .087 .058
10 1095 1155 289 113 806 1042 1031 1151 314 164 742 1038 0 0 303 168 119 136 100 100 100 100 1848 1780 .774 1.293 1.399 1.348 1.383 1.446 32 220 1.215 .87 70 3230 19090 69 76 255 262 0 1414 138 1275 1.582 1409 1270 .632 1.712 .662 .776
11 1099 3534 241 50 858 3484 1039 3557 241 102 798 3507 0 0 267 356 65 167 100 100 100 100 4342 4305 .246 4.061 4.395 4.222 4.377 1.372 32 214 4.35 .9 70 3400 19090 69 76 272 279 0 4325 61 4264 4.969 4353 4292 .201 5.378 2.313 2.427
12 826 940 238 48 588 892 870 984 240 57 632 936 0 0 206 260 60 48 94 100 92 100 1480 1568 .659 1.517 1.481 1.624 1.56 1.535 52 281 1.499 .93 80 3550 19090 69 77 287 295 0 1150 59 1092 1.857 1204 1145 .539 1.812 .893 .858
13 756 2616 230 46 526 2570 704 2013 242 48 474 1967 0 0 421 1978 78 10 81 100 75 100 3096 2441 .205 4.886 4.15 4.887 5.043 2.109 32 201 5.408 .88 70 3700 19080 68 75 302 309 0 3201 56 3145 5.979 2464 2407 .167 5.079 2.58 2.344
14 810 384 245 43 565 341 837 421 252 45 592 378 0 0 232 140 95 10 93 100 90 100 906 970 1.657 .604 .639 .627 .658 1.453 32 134 .541 .89 60 3860 19080 69 75 319 325 0 470 53 417 .739 515 463 1.354 .781 -.437 -.356
15 867 473 226 44 641 429 894 453 229 45 668 409 0 0 173 178 55 9 100 100 100 100 1070 1077 1.494 .669 .612 .624 .692 1.484 32 148 .673 .91 60 4030 19090 70 76 336 342 0 579 54 525 .819 554 501 1.221 .749 -.288 -.416
16 931 719 237 46 694 673 938 732 242 53 701 686 0 0 156 141 56 20 100 100 100 100 1367 1387 1.031 .97 .979 .972 1.002 1.242 32 148 .942 .93 60 4180 19090 70 76 351 357 0 880 56 824 1.187 896 840 .843 1.198 .247 .26
17 1264 4512 233 47 1031 4465 1211 4112 235 56 978 4065 0 0 478 2370 53 28 100 100 96 100 5496 5043 .231 4.331 4.156 4.141 4.245 1.555 32 220 4.788 .92 70 4340 19090 69 76 366 373 0 5522 58 5464 5.3 5032 4975 .189 5.087 2.406 2.347
18 1077 611 240 51 837 560 1042 619 245 54 802 568 0 0 154 113 64 17 100 100 100 100 1397 1370 1.495 .669 .708 .666 .687 1.307 32 148 .64 .91 60 4500 19090 70 76 383 389 0 748 62 685 .819 758 695 1.221 .867 -.288 -.206
19 983 2709 230 51 753 2658 967 2585 235 64 737 2534 0 0 203 494 61 76 100 100 100 100 3411 3271 .283 3.53 3.438 3.607 3.527 1.247 32 206 3.535 .95 70 4660 19080 68 75 398 405 0 3315 62 3253 4.32 3164 3101 .231 4.208 2.111 2.073
20 1537 4311 260 61 1277 4250 1522 4314 274 124 1262 4253 0 0 281 345 91 237 100 100 100 100 5527 5515 .3 3.328 3.37 3.395 3.329 1.207 32 201 3.264 .94 70 4820 19080 68 75 414 421 0 5276 75 5201 4.073 5280 5205 .246 4.124 2.026 2.044

Total number of rows: 21504

Table truncated, full table size 4653 Kbytes.




Supplementary data files not provided
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