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Sample GSM62235 Query DataSets for GSM62235
Status Public on Jun 25, 2005
Title vhl-1 3N vs. vhl-1 3H
Sample type RNA
 
Channel 1
Source name vhl-1 3H
Organism Caenorhabditis elegans
Characteristics vhl-1 3H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name vhl-1 3N
Organism Caenorhabditis elegans
Characteristics vhl-1 3N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27042.gif; format: GIF
Data processing Value is Log (base 2) of the ratio of the median of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Jun 24, 2005
Last update date Nov 23, 2005
Contact name Min Jiang
E-mail(s) [email protected]
Phone 650-725-7612
Fax 650-725-7739
Organization name Stanford University
Street address -
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL2569
Series (1)
GSE2836 Hypoxia response

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
LOG_RAT2N_MEAN 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
VALUE same as UNF_VALUE but with flagged values removed
UNF_VALUE 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 LOG_RAT2N_MEAN VALUE UNF_VALUE
1 13176 20171 67 126 13109 20045 14433 20792 96 139 14366 20666 0 0 5809 7771 181 67 95 100 93 100 33154 35032 .654 1.529 1.439 4.535 1.56 12.719 80 426 1.428 .95 100 1620 19780 77 87 93 103 0 28410 177 28232 2.154 29285 29107 .464 2.026 1.107 1.019 1.019
2 8624 11327 64 119 8560 11208 9340 11998 70 136 9276 11879 0 0 2483 3378 45 92 100 100 100 100 19768 21155 .764 1.309 1.281 1.351 1.31 .406 52 343 1.224 .96 90 1770 19780 77 86 108 117 0 15954 168 15786 1.844 16899 16731 .542 1.804 .883 .851 .851
3 185 237 61 140 124 97 183 244 67 150 122 104 0 0 48 60 24 65 100 75 96 31 221 226 1.278 .782 .852 .994 .898 .625 32 220 .564 .48 70 1940 19770 77 84 126 133 0 334 197 137 1.102 344 146 .908 1.201 .14 .264 .264
4 2380 1243 64 145 2316 1098 2700 1281 68 151 2636 1136 0 0 989 618 26 59 100 98 100 94 3414 3772 2.109 .474 .431 .472 .427 .198 52 304 .465 .92 90 2100 19770 76 85 141 150 0 1751 204 1546 .668 1804 1600 1.498 .607 -.583 -.72 -.72
5 12189 8797 64 134 12125 8663 12268 9747 68 140 12204 9613 0 0 9275 7210 25 56 100 100 100 100 20788 21817 1.4 .714 .788 .64 .661 .39 80 512 .708 .97 110 2270 19760 74 85 157 168 0 12390 189 12201 1.006 13728 13539 .994 1.109 .009 .15 .15
6 1301 1322 66 123 1235 1199 1297 1332 76 130 1231 1209 0 0 715 557 42 52 100 100 100 100 2434 2440 1.03 .971 .982 1.246 1.009 .676 12 87 .849 .9 50 2420 19760 77 82 175 180 0 1862 173 1689 1.367 1876 1703 .731 1.383 .451 .468 .468
7 10635 6191 61 124 10574 6067 11841 5353 68 133 11780 5229 0 0 5407 4327 44 51 100 100 100 100 16641 17009 1.743 .574 .444 .544 .578 .288 52 366 .601 .94 90 2580 19770 76 85 189 198 0 8720 175 8545 .808 7539 7365 1.237 .625 -.307 -.678 -.678
8 631 832 63 150 568 682 341 599 66 155 278 449 0 0 658 623 21 51 87 93 81 90 1250 727 .833 1.201 1.615 2.879 1.498 4.245 32 160 .938 .9 60 2740 19760 77 83 207 213 0 1172 211 961 1.691 844 632 .591 2.275 .758 1.186 1.186
9 351 458 63 148 288 310 358 421 69 153 295 273 0 0 143 155 28 57 95 97 92 96 598 568 .929 1.076 .925 1.376 1.034 1.263 80 459 .924 .83 100 2910 19770 76 86 222 232 0 645 208 437 1.516 593 385 .66 1.303 .6 .382 .382
10 1127 1133 67 151 1060 982 1141 1077 70 153 1074 926 0 0 434 435 25 55 100 100 100 100 2042 2000 1.079 .926 .862 1.098 .907 .874 52 308 .833 .9 90 3060 19760 75 84 237 246 0 1596 213 1383 1.305 1517 1304 .766 1.214 .384 .28 .28
11 5311 1827 66 144 5245 1683 5147 1605 68 146 5081 1461 0 0 2621 1230 22 54 100 100 100 97 6928 6542 3.116 .321 .288 .31 .31 .172 120 564 .322 .91 120 3220 19730 71 83 252 264 0 2573 203 2370 .452 2261 2058 2.213 .405 -1.146 -1.304 -1.304
12 561 1011 61 141 500 870 561 1004 65 147 500 863 0 0 155 239 22 54 100 100 100 100 1370 1363 .575 1.74 1.726 1.913 1.74 .846 52 357 1.506 .9 90 3390 19760 75 84 270 279 0 1424 199 1225 2.451 1414 1215 .408 2.431 1.293 1.282 1.282
13 5867 3740 58 127 5809 3613 6343 3531 67 133 6285 3404 0 0 3170 3126 61 51 100 97 100 96 9422 9689 1.608 .622 .542 .515 .503 .325 80 518 .679 .91 110 3560 19760 74 85 286 297 0 5268 179 5089 .876 4973 4794 1.142 .763 -.191 -.391 -.391
14 232 233 61 141 171 92 228 212 65 143 167 71 0 0 51 96 24 50 100 62 100 34 263 238 1.859 .538 .425 .759 .538 .652 32 158 .416 .42 60 3700 19760 77 83 303 309 0 328 199 130 .758 299 100 1.32 .599 -.4 -.74 -.74
15 190 299 57 129 133 170 172 274 60 134 115 145 0 0 70 149 20 52 98 75 94 65 303 260 .782 1.278 1.261 1.438 1.204 1.004 52 322 1.114 .68 80 3860 19760 76 84 318 326 0 421 182 239 1.8 386 204 .555 1.776 .848 .829 .829
16 440 327 58 127 382 200 422 327 65 129 364 200 0 0 137 112 35 49 100 90 98 80 582 564 1.91 .524 .549 .541 .537 .28 52 286 .48 .76 80 4030 19750 75 83 335 343 0 461 179 282 .737 461 282 1.356 .774 -.439 -.37 -.37
17 9414 6386 58 125 9356 6261 11034 7690 64 129 10976 7565 0 0 4881 3275 35 51 100 100 100 100 15617 18541 1.494 .669 .689 .697 .64 .346 52 341 .621 .96 90 4180 19740 73 82 349 358 0 8994 176 8818 .943 10831 10655 1.061 .971 -.085 -.043 -.043
18 807 681 58 131 749 550 804 671 64 133 746 540 0 0 217 194 28 53 100 100 100 100 1299 1286 1.362 .734 .724 .757 .729 .251 52 338 .659 .88 90 4340 19750 74 83 365 374 0 959 185 775 1.034 945 761 .967 1.02 .049 .028 .028
19 1994 865 58 134 1936 731 2153 912 63 141 2095 778 0 0 1305 582 22 55 99 90 98 83 2667 2873 2.648 .378 .371 .464 .357 .522 120 552 .364 .91 120 4500 19730 71 83 380 392 0 1218 189 1030 .532 1285 1096 1.88 .523 -.911 -.935 -.935
20 2085 1342 60 140 2025 1202 2241 1317 65 146 2181 1177 0 0 756 667 28 54 98 97 98 97 3227 3358 1.685 .594 .54 .617 .561 .348 80 403 .588 .91 100 4670 19750 74 84 398 408 0 1890 197 1693 .836 1855 1658 1.196 .76 -.258 -.396 -.396

Total number of rows: 21888

Table truncated, full table size 5032 Kbytes.




Supplementary data files not provided
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