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Sample GSM62234 Query DataSets for GSM62234
Status Public on Jun 25, 2005
Title hif-1 1N vs. hif-1 1H
Sample type RNA
 
Channel 1
Source name hif-1 1H
Organism Caenorhabditis elegans
Characteristics hif-1 1H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name hif-1 1N
Organism Caenorhabditis elegans
Characteristics hif-1 1N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27033.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) mjiang@cmgm.stanford.edu
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 11960 16880 118 392 11842 16488 11962 11105 245 455 11844 10713 0 0 8250 13911 513 342 87 97 87 96 28330 22557 .718 1.392 .905 2.871 1.349 5.632 80 437 1.433 .95 100 1940 18790 79 89 102 112 0 21641 503 21138 1.785 14237 13735 .56 1.16 .836 .214 .214
2 11063 10764 125 403 10938 10361 14268 13039 385 494 14143 12636 0 0 7784 6457 583 358 75 93 75 87 21299 26779 1.056 .947 .893 4.709 .975 11.86 32 206 .878 .98 70 2110 18780 79 86 120 127 0 13800 517 13283 1.214 16717 16200 .823 1.145 .28 .196 .196
3 546 885 104 357 442 528 472 858 115 383 368 501 0 0 218 312 46 170 100 87 100 68 970 869 .837 1.195 1.361 1.259 1.217 .658 32 216 1.098 .78 70 2270 18790 80 87 136 143 0 1135 458 677 1.532 1100 642 .653 1.745 .615 .804 .804
4 2515 2126 118 359 2397 1767 2809 2260 134 393 2691 1901 0 0 932 1015 97 225 98 96 98 90 4164 4592 1.357 .737 .706 .83 .679 .796 52 270 .723 .9 80 2420 18810 82 90 151 159 0 2726 460 2265 .945 2897 2437 1.058 .906 -.081 -.143 -.143
5 7748 12718 117 344 7631 12374 7029 10759 132 357 6912 10415 0 0 6307 10690 57 161 100 98 97 93 20005 17327 .617 1.622 1.507 2.074 1.568 2.997 80 437 1.613 .97 100 2580 18790 79 89 166 176 0 16305 441 15864 2.079 13794 13353 .481 1.932 1.056 .95 .95
6 3139 2547 134 353 3005 2194 3494 2776 152 366 3360 2423 0 0 1727 1322 63 141 100 91 100 91 5199 5783 1.37 .73 .721 .754 .674 .426 12 98 .709 .96 50 2750 18800 82 87 185 190 0 3265 453 2813 .936 3559 3106 1.068 .925 -.095 -.113 -.113
7 18400 11074 126 338 18274 10736 20314 11830 150 354 20188 11492 0 0 5180 3688 110 137 100 100 100 100 29010 31680 1.702 .588 .569 .583 .588 .088 32 234 .568 .97 70 2910 18810 82 89 200 207 0 14197 433 13764 .753 15167 14733 1.328 .73 -.409 -.454 -.454
8 264 515 124 372 140 143 195 443 149 385 71 71 0 0 249 323 175 161 18 30 11 18 283 142 .979 1.021 1 5.54 2.093 10.815 80 447 .859 .57 100 3080 18810 81 91 216 226 0 660 477 183 1.31 568 91 .764 1.282 .389 .358 .358
9 924 1179 123 372 801 807 957 1140 144 385 834 768 0 0 343 389 163 155 95 97 90 88 1608 1602 .993 1.007 .921 1.37 1.028 1.59 80 416 .734 .72 100 3240 18810 81 91 232 242 0 1512 477 1035 1.292 1462 985 .774 1.181 .369 .24 .24
10 587 1161 129 368 458 793 566 1144 140 394 437 776 0 0 209 363 58 166 98 96 98 90 1251 1213 .578 1.731 1.776 1.893 1.867 .807 52 266 1.414 .79 80 3390 18810 82 90 248 256 0 1488 472 1017 2.22 1467 995 .45 2.277 1.15 1.187 1.187
11 5424 4274 137 388 5287 3886 6036 4660 181 420 5899 4272 0 0 2391 1991 295 214 98 100 98 98 9173 10171 1.361 .735 .724 .759 .752 .263 80 432 .678 .94 100 3550 18800 80 90 263 273 0 5479 497 4982 .942 5974 5477 1.061 .928 -.086 -.107 -.107
12 746 1188 130 375 616 813 738 1186 141 374 608 811 0 0 234 316 61 144 100 100 100 94 1429 1419 .758 1.32 1.334 1.494 1.246 .817 52 367 1.108 .8 90 3720 18820 82 91 280 289 0 1523 481 1042 1.692 1521 1040 .591 1.71 .759 .774 .774
13 4937 4635 130 386 4807 4249 4018 3895 139 402 3888 3509 0 0 3411 3239 53 154 98 96 98 93 9056 7397 1.131 .884 .903 1.04 .885 .842 80 461 .882 .97 100 3880 18820 82 92 296 306 0 5942 495 5447 1.133 4994 4499 .882 1.157 .18 .21 .21
14 471 776 135 418 336 358 455 777 148 430 320 359 0 0 130 247 56 161 100 81 100 53 694 679 .939 1.065 1.122 1.244 1.241 .84 32 224 .662 .5 70 4040 18820 83 90 313 320 0 995 536 459 1.366 996 460 .732 1.438 .45 .524 .524
15 533 896 161 477 372 419 555 973 191 485 394 496 0 0 201 214 87 226 91 75 75 58 791 890 .888 1.126 1.259 1.725 1.074 2.394 12 90 .847 .59 50 4180 18810 83 88 328 333 0 1149 612 537 1.444 1247 636 .693 1.614 .53 .691 .691
16 875 1103 130 405 745 698 815 997 155 419 685 592 0 0 379 428 104 184 100 93 100 78 1443 1277 1.067 .937 .864 1.076 .925 .65 32 230 .724 .7 70 4360 18820 83 90 345 352 0 1414 519 895 1.201 1278 759 .833 1.108 .264 .148 .148
17 16316 14066 125 394 16191 13672 18674 16348 135 408 18549 15954 0 0 6465 5639 63 175 100 100 100 100 29863 34503 1.184 .844 .86 .877 .852 .246 52 372 .824 .97 90 4520 18820 82 91 360 369 0 18033 505 17528 1.083 20959 20454 .924 1.103 .114 .141 .141
18 1769 1747 131 405 1638 1342 1777 1678 158 414 1646 1273 0 0 410 618 141 169 100 100 100 100 2980 2919 1.221 .819 .773 .827 .802 .322 52 310 .804 .87 80 4680 18830 84 92 377 385 0 2240 519 1721 1.05 2151 1632 .952 .992 .071 -.012 -.012
19 3252 2357 128 393 3124 1964 3623 2465 140 408 3495 2072 0 0 1267 939 59 171 100 98 98 93 5088 5567 1.591 .629 .593 .694 .602 .502 80 427 .614 .93 100 4850 18820 82 92 393 403 0 3022 504 2518 .806 3160 2656 1.241 .76 -.311 -.396 -.396
20 2313 2275 128 374 2185 1901 2386 2263 138 380 2258 1889 0 0 758 657 63 146 100 100 100 98 4086 4147 1.149 .87 .837 .951 .907 .374 52 338 .77 .91 90 4990 18820 82 91 407 416 0 2917 479 2437 1.115 2901 2422 .897 1.073 .158 .101 .101

Total number of rows: 21888

Table truncated, full table size 5116 Kbytes.




Supplementary data files not provided

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