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Sample GSM62232 Query DataSets for GSM62232
Status Public on Jun 25, 2005
Title vhl-1 1N vs. vhl-1 1H
Sample type RNA
 
Channel 1
Source name vhl-1 1H
Organism Caenorhabditis elegans
Characteristics vhl-1 1H
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name vhl-1 1N
Organism Caenorhabditis elegans
Characteristics vhl-1 1N
Extracted molecule total RNA
Label Cy5
 
 
Description Image: http://genome-www5.stanford.edu/MicroArray/gifs/2002-03/27040.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 11240 4778 75 173 11165 4605 9337 3445 77 173 9262 3272 0 0 8967 4024 22 71 100 100 100 96 15770 12534 2.425 .412 .353 .506 .414 .429 32 120 .412 .96 60 1480 19210 78 84 105 111 0 8098 293 7805 .699 5839 5546 1.43 .599 -.516 -.74 -.74
2 7490 2914 69 165 7421 2749 5861 2126 73 167 5792 1961 0 0 5247 2035 24 69 100 100 100 96 10170 7753 2.7 .37 .339 .448 .391 .37 32 160 .359 .95 60 1640 19220 79 85 121 127 0 4939 280 4659 .628 3603 3324 1.593 .574 -.671 -.801 -.801
3 116 179 70 165 46 14 77 169 73 171 7 4 0 0 97 69 22 74 35 21 25 3 60 11 3.286 .304 .571 4.217 1.71 8.406 80 466 .244 .19 100 1820 19230 78 88 137 147 0 303 280 24 .516 286 7 1.939 .969 -.955 -.046 -.046
4 2340 1328 70 165 2270 1163 1512 1029 75 168 1442 864 0 0 2157 1176 22 81 93 96 93 75 3433 2306 1.952 .512 .599 2.036 .585 6.461 32 155 .5 .94 60 1970 19220 79 85 154 160 0 2251 280 1971 .868 1744 1464 1.152 1.016 -.204 .022 .022
5 17039 6183 72 177 16967 6006 22923 7528 402 408 22851 7351 0 0 10761 3889 4123 2404 78 71 71 62 22973 30202 2.825 .354 .322 .402 .368 .203 32 206 .34 .95 70 2120 19210 77 84 168 175 0 10480 300 10180 .6 12759 12459 1.667 .545 -.737 -.875 -.875
6 358 333 68 169 290 164 92 203 73 175 24 34 0 0 656 347 27 72 47 42 35 22 454 58 1.768 .566 1.417 3.978 .901 7.696 80 436 .487 .82 100 2300 19230 78 88 185 195 0 564 286 278 .959 344 58 1.043 2.401 -.061 1.264 1.264
7 12517 4544 65 173 12452 4371 13065 3995 70 171 13000 3822 0 0 7711 2883 23 65 100 100 100 96 16823 16822 2.849 .351 .294 .435 .368 .324 32 156 .34 .95 60 2440 19230 80 86 201 207 0 7702 293 7408 .595 6771 6478 1.681 .498 -.749 -1.005 -1.005
8 105 191 67 165 38 26 82 179 182 289 15 14 0 0 69 93 952 1004 0 0 0 0 64 29 1.462 .684 .933 4.707 1.546 6.584 80 429 .946 .96 100 2620 19240 79 89 217 227 0 324 280 44 1.16 303 24 .862 1.582 .214 .662 .662
9 958 977 65 153 893 824 964 1013 68 161 899 860 0 0 280 324 20 77 100 98 100 98 1717 1759 1.084 .923 .957 .967 1.001 .355 52 277 .867 .9 80 2770 19230 79 87 233 241 0 1656 259 1397 1.564 1717 1458 .639 1.621 .645 .697 .697
10 2318 1592 66 158 2252 1434 2371 1718 69 166 2305 1560 0 0 655 565 23 76 100 100 100 100 3686 3865 1.57 .637 .677 .639 .62 .172 32 225 .572 .93 70 2920 19240 80 87 248 255 0 2698 268 2431 1.079 2912 2644 .927 1.147 .11 .198 .198
11 5100 1847 67 153 5033 1694 5765 1839 71 159 5698 1686 0 0 3896 1318 28 68 98 92 97 88 6727 7384 2.971 .337 .296 .514 .328 .824 80 469 .322 .95 100 3090 19240 79 89 264 274 0 3131 259 2871 .57 3117 2858 1.753 .502 -.81 -.996 -.996
12 1152 785 64 143 1088 642 1196 773 68 156 1132 630 0 0 389 326 19 71 100 96 100 94 1730 1762 1.695 .59 .557 .6 .544 .263 52 297 .559 .88 80 3250 19240 80 88 281 289 0 1331 242 1088 1 1310 1068 1 .943 0 -.084 -.084
13 6131 3086 65 149 6066 2937 5821 3159 69 158 5756 3010 0 0 5235 2536 22 71 100 94 100 80 9003 8766 2.065 .484 .523 .694 .49 .873 52 303 .462 .95 80 3410 19230 79 87 297 305 0 5231 253 4978 .821 5354 5102 1.219 .886 -.285 -.174 -.174
14 290 302 67 169 223 133 297 295 316 516 230 126 0 0 106 117 964 1312 0 0 0 0 356 356 1.677 .596 .548 .849 .653 .809 32 160 .525 .56 60 3570 19240 81 87 314 320 0 512 286 225 1.011 500 214 .989 .929 .016 -.107 -.107
15 310 312 63 150 247 162 311 297 66 155 248 147 0 0 64 106 22 64 100 81 100 59 409 395 1.525 .656 .593 .736 .633 .48 32 170 .542 .6 60 3730 19250 82 88 330 336 0 529 254 275 1.112 503 249 .9 1.005 .153 .007 .007
16 875 461 64 162 811 299 868 450 71 174 804 288 0 0 252 142 35 73 100 96 100 90 1110 1092 2.712 .369 .358 .421 .394 .245 32 170 .304 .7 60 3890 19250 82 88 346 352 0 781 275 507 .625 763 488 1.6 .607 -.678 -.72 -.72
17 12330 7237 62 165 12268 7072 14521 8902 65 170 14459 8737 0 0 9626 5505 20 73 100 100 100 98 19340 23196 1.735 .576 .604 .74 .599 .681 52 302 .549 .96 80 4050 19240 80 88 361 369 0 12266 280 11986 .977 15088 14808 1.023 1.024 -.033 .034 .034
18 1265 821 62 154 1203 667 1335 871 69 166 1273 717 0 0 500 315 39 74 100 100 100 94 1870 1990 1.804 .554 .563 .618 .588 .355 52 300 .515 .89 80 4210 19240 80 88 377 385 0 1392 261 1131 .94 1476 1215 1.064 .955 -.09 -.067 -.067
19 4663 1558 63 156 4600 1402 4988 1468 67 161 4925 1312 0 0 1264 559 24 64 100 98 100 98 6002 6237 3.281 .305 .266 .304 .316 .094 52 295 .302 .94 80 4380 19240 80 88 394 402 0 2641 264 2376 .517 2488 2224 1.936 .452 -.953 -1.147 -1.147
20 3405 1976 63 152 3342 1824 3865 2244 69 159 3802 2092 0 0 1385 781 33 67 100 100 100 100 5166 5894 1.832 .546 .55 .598 .574 .217 32 194 .506 .95 70 4520 19230 79 86 408 415 0 3349 258 3092 .925 3803 3546 1.081 .933 -.112 -.101 -.101

Total number of rows: 21888

Table truncated, full table size 4992 Kbytes.




Supplementary data files not provided

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