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Sample GSM62231 Query DataSets for GSM62231
Status Public on Jun 25, 2005
Title wt 1N vs. wt 1H
Sample type RNA
 
Channel 1
Source name wt 1H
Organism Caenorhabditis elegans
Characteristics wt 1H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name wt 1N
Organism Caenorhabditis elegans
Characteristics wt 1N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27032.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 14970 14032 121 266 14849 13766 14054 13161 196 298 13933 12895 0 0 11590 10767 324 175 88 94 86 92 28615 26828 1.079 .927 .926 1.636 .924 3.08 52 280 .882 .97 80 1910 19750 99 107 67 75 0 12202 231 11970 .806 11444 11213 1.24 .805 -.311 -.313 -.313
2 5404 5824 136 277 5268 5547 5495 6312 190 300 5359 6035 0 0 3305 3769 299 152 94 98 90 96 10815 11394 .95 1.053 1.126 1.21 1.063 1.039 52 309 1.033 .95 80 2080 19760 100 108 84 92 0 5064 241 4823 .916 5489 5248 1.092 .979 -.127 -.03 -.03
3 467 897 117 286 350 611 460 834 124 290 343 548 0 0 148 345 38 125 100 90 96 84 961 891 .573 1.746 1.598 1.927 1.623 1.375 32 170 1.469 .78 60 2240 19760 101 107 101 107 0 780 249 531 1.518 725 477 .659 1.389 .602 .474 .474
4 2379 1680 124 264 2255 1416 2578 1777 151 273 2454 1513 0 0 831 686 140 117 100 100 100 93 3671 3967 1.593 .628 .617 .652 .627 .327 32 176 .565 .89 60 2410 19770 102 108 118 124 0 1461 230 1231 .546 1545 1316 1.831 .536 -.873 -.899 -.899
5 12338 20802 124 274 12214 20528 13698 23403 149 291 13574 23129 0 0 4680 8821 139 123 100 100 100 100 32742 36703 .595 1.681 1.704 1.689 1.711 .438 52 393 1.693 .98 90 2570 19760 99 108 132 141 0 18089 238 17850 1.461 20350 20112 .684 1.482 .547 .567 .567
6 2204 2822 134 300 2070 2522 2614 2814 141 306 2480 2514 0 0 1032 1217 49 122 100 100 100 100 4592 4994 .821 1.218 1.014 1.414 1.352 .53 12 90 1.019 .93 50 2730 19750 100 105 150 155 0 2454 261 2193 1.059 2447 2186 .944 .881 .083 -.182 -.182
7 14631 15650 130 292 14501 15358 17543 18212 154 307 17413 17920 0 0 6198 7814 120 120 100 100 100 100 29859 35333 .944 1.059 1.029 1.038 .996 .262 32 230 1.044 .97 70 2900 19760 100 107 166 173 0 13609 254 13355 .921 15837 15583 1.086 .895 -.119 -.16 -.16
8 394 739 122 296 272 443 327 696 130 289 205 400 0 0 215 373 44 105 90 81 84 75 715 605 .614 1.629 1.951 2.139 1.861 1.628 32 155 1.396 .79 60 3060 19750 100 106 183 189 0 643 257 385 1.416 605 348 .706 1.697 .502 .763 .763
9 913 1832 123 278 790 1554 977 1850 134 294 854 1572 0 0 323 648 65 166 98 100 96 97 2344 2426 .508 1.967 1.841 2.272 1.956 1.321 80 432 1.767 .89 100 3210 19760 99 109 196 206 0 1593 242 1351 1.711 1609 1367 .585 1.601 .774 .679 .679
10 856 1292 133 292 723 1000 773 1148 139 305 640 856 0 0 303 454 51 123 100 100 96 100 1723 1496 .723 1.383 1.338 1.493 1.247 .617 32 218 1.198 .87 70 3360 19760 100 107 212 219 0 1123 254 870 1.203 998 744 .831 1.163 .266 .218 .218
11 6098 4425 124 283 5974 4142 6452 5125 135 297 6328 4842 0 0 3609 2888 71 120 100 96 100 96 10116 11170 1.442 .693 .765 .623 .676 .277 80 533 .678 .96 110 3530 19740 96 107 227 238 0 3848 246 3602 .603 4457 4210 1.659 .665 -.73 -.588 -.588
12 641 870 114 284 527 586 609 803 122 290 495 519 0 0 231 437 43 112 100 96 100 86 1113 1014 .899 1.112 1.048 1.137 1.031 .545 52 369 .993 .78 90 3700 19760 99 108 245 254 0 757 247 510 .967 698 451 1.034 .912 -.049 -.133 -.133
13 4962 5823 119 302 4843 5521 5836 5737 127 306 5717 5435 0 0 3001 3953 53 112 100 100 100 100 10364 11152 .877 1.14 .951 1.135 1.132 .528 52 314 1.167 .97 80 3860 19760 100 108 262 270 0 5063 263 4801 .991 4989 4726 1.009 .827 -.013 -.275 -.275
14 430 785 106 269 324 516 400 698 114 269 294 429 0 0 147 367 43 115 100 93 100 87 840 723 .628 1.593 1.459 1.738 1.518 1.161 32 165 1.285 .7 60 4020 19760 101 107 279 285 0 683 234 449 1.385 607 373 .722 1.269 .47 .344 .344
15 422 866 102 267 320 599 384 697 109 279 282 430 0 0 234 565 42 119 92 88 84 73 919 712 .534 1.872 1.525 2.133 1.618 1.879 52 301 1.661 .78 80 4160 19750 99 107 292 300 0 753 232 521 1.628 606 374 .614 1.326 .703 .407 .407
16 660 898 109 250 551 648 671 876 170 276 562 626 0 0 204 242 269 137 87 100 56 93 1199 1188 .85 1.176 1.114 1.431 1.164 1.125 32 170 .944 .81 60 4330 19760 101 107 310 316 0 781 217 563 1.023 762 544 .978 .969 .032 -.046 -.046
17 8350 10489 120 260 8230 10229 10385 12400 210 287 10265 12140 0 0 4780 5277 367 148 96 100 92 100 18459 22405 .805 1.243 1.183 2.656 1.246 5.353 52 374 1.165 .96 90 4490 19760 99 108 324 333 0 9121 226 8895 1.081 10783 10557 .925 1.028 .112 .04 .04
18 1636 2440 112 275 1524 2165 1698 2263 116 280 1586 1988 0 0 646 1369 49 116 100 100 100 98 3689 3574 .704 1.421 1.253 1.439 1.173 .857 52 296 1.425 .89 80 4660 19770 101 109 342 350 0 2122 239 1883 1.235 1968 1729 .81 1.09 .305 .124 .124
19 2186 2031 103 261 2083 1770 2295 2006 110 274 2192 1745 0 0 863 901 45 109 97 100 97 98 3853 3937 1.177 .85 .796 1.279 .873 2.937 80 433 .818 .92 100 4810 19760 99 109 356 366 0 1766 227 1539 .739 1744 1517 1.353 .692 -.437 -.531 -.531
20 1165 1659 105 255 1060 1404 1193 1644 112 266 1088 1389 0 0 307 459 43 103 100 100 100 100 2464 2477 .755 1.325 1.277 1.39 1.241 .463 52 345 1.216 .91 90 4970 19760 99 108 372 381 0 1443 222 1221 1.152 1430 1208 .868 1.11 .204 .151 .151

Total number of rows: 21888

Table truncated, full table size 5131 Kbytes.




Supplementary data files not provided

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