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Sample GSM64840 Query DataSets for GSM64840
Status Public on Jul 20, 2005
Title hif-1 (red, channel 2) vs. hif-1; vhl-1 (green, channel 1) repeat no. 2
Sample type RNA
 
Channel 1
Source name hif-1; vhl-1
Organism Caenorhabditis elegans
Characteristics hif-1; vhl-1
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name hif-1
Organism Caenorhabditis elegans
Characteristics hif-1
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: C. elegans, C. elegans
Image: http://smd.stanford.edu/MicroArray/gifs/2002-04/27321.gif
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 Jul 19, 2005
Last update date Sep 22, 2006
Organization Stanford Microarray Database (SMD)
E-mail(s) array@genome.stanford.edu
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 GPL2647
Series (1)
GSE2963 Genetic Analysis of Pathways Regulated by the von Hippel-Lindau Tumor Suppressor in Caenorhabditis elegans

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
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 7385 5250 98 170 7287 5080 7236 5193 102 181 7138 5023 0 0 4897 3320 36 83 100 100 100 100 12367 12161 1.434 .697 .704 1.209 .69 2.295 52 268 .673 .98 80 1610 19390 79 87 75 83 0 7095 230 6865 .942 7018 6788 1.061 .951 -.086 -.073
2 3455 3048 90 169 3365 2879 3483 3517 92 180 3393 3348 0 0 2099 1553 27 68 100 100 100 100 6244 6741 1.169 .856 .987 1.385 .871 2.157 52 342 .791 .97 90 1780 19390 78 87 91 100 0 4119 228 3891 1.156 4753 4524 .865 1.333 .209 .415
3 277 370 86 164 191 206 263 369 91 174 177 205 0 0 91 75 30 64 100 98 94 82 397 382 .927 1.079 1.158 1.336 1.11 .82 52 347 .784 .69 90 1940 19400 79 88 107 116 0 500 222 278 1.457 499 277 .686 1.565 .543 .646
4 3131 2830 85 161 3046 2669 3284 3015 92 171 3199 2854 0 0 1657 1623 34 66 100 100 100 100 5715 6053 1.141 .876 .892 .863 .837 .288 52 336 .884 .98 90 2110 19380 77 86 124 133 0 3824 218 3607 1.184 4074 3857 .845 1.206 .244 .27
5 7586 1839 85 161 7501 1678 9310 2075 92 167 9225 1914 0 0 3302 680 37 66 100 100 100 100 9179 11139 4.47 .224 .207 .256 .223 .124 52 351 .214 .97 90 2270 19380 77 86 140 149 0 2485 218 2268 .302 2804 2586 3.308 .28 -1.726 -1.835
6 928 979 82 168 846 811 887 938 89 173 805 770 0 0 602 581 39 61 100 100 100 93 1657 1575 1.043 .959 .957 1.045 .992 .472 32 220 .908 .95 70 2430 19390 79 86 157 164 0 1323 227 1096 1.295 1268 1041 .772 1.293 .373 .37
7 4631 5095 91 166 4540 4929 4938 5604 100 184 4847 5438 0 0 2334 2643 94 99 100 100 100 100 9469 10285 .921 1.086 1.122 1.286 1.062 1.204 32 206 1.07 .98 70 2590 19380 78 85 173 180 0 6885 224 6661 1.467 7573 7349 .682 1.516 .553 .6
8 163 291 86 163 77 128 121 248 107 180 35 85 0 0 110 144 96 94 26 46 15 25 205 120 .602 1.662 2.429 4.008 1.64 10.472 80 434 1.01 .69 100 2760 19400 79 89 189 199 0 393 220 173 2.246 335 115 .445 3.282 1.168 1.715
9 15178 13706 94 179 15084 13527 17769 15310 276 284 17675 15131 0 0 6414 6075 726 452 100 100 96 97 28611 32806 1.115 .897 .856 .911 .906 .268 80 414 .893 .98 100 2910 19400 79 89 204 214 0 18522 242 18280 1.212 20689 20447 .825 1.157 .277 .21
10 1288 2164 90 178 1198 1986 1368 2210 103 203 1278 2032 0 0 308 415 75 114 100 100 100 100 3184 3310 .603 1.658 1.59 1.707 1.698 .313 32 208 1.465 .95 70 3060 19390 79 86 220 227 0 2924 241 2684 2.24 2986 2746 .446 2.149 1.164 1.103
11 5460 3405 84 160 5376 3245 5699 3581 90 171 5615 3421 0 0 2928 1856 40 87 100 98 100 97 8621 9036 1.657 .604 .609 .625 .617 .274 80 505 .6 .98 110 3230 19380 76 87 235 246 0 4601 216 4385 .816 4839 4623 1.226 .823 -.294 -.28
12 610 1062 84 158 526 904 631 1019 89 171 547 861 0 0 230 379 41 114 100 100 98 98 1430 1408 .582 1.719 1.574 1.909 1.794 .831 80 453 1.579 .93 100 3390 19400 79 89 252 262 0 1435 214 1222 2.322 1377 1164 .431 2.127 1.216 1.089
13 3753 3843 91 163 3662 3680 2699 3031 1260 1337 2608 2868 0 0 2668 2729 4923 4912 37 32 0 0 7342 5476 .995 1.005 1.1 1.21 1.031 .873 80 454 .964 .97 100 3570 19390 78 88 270 280 0 5193 220 4973 1.358 4096 3876 .736 1.486 .441 .572
14 315 332 93 154 222 178 312 335 97 165 219 181 0 0 92 121 30 69 100 75 100 65 400 400 1.247 .802 .826 .832 .827 .51 32 148 .601 .62 60 3710 19400 81 87 286 292 0 449 208 241 1.084 453 245 .923 1.117 .116 .159
15 359 370 90 166 269 204 348 344 96 179 258 178 0 0 137 153 46 91 94 75 88 46 473 436 1.319 .758 .69 .92 .856 .767 52 321 .749 .72 80 3860 19410 81 89 300 308 0 500 224 276 1.025 465 241 .976 .932 .035 -.101
16 670 720 92 170 578 550 673 724 98 184 581 554 0 0 132 177 36 69 100 100 100 100 1128 1135 1.051 .952 .954 .967 .973 .285 32 214 .826 .88 70 4040 19400 80 87 318 325 0 973 230 743 1.286 978 749 .778 1.289 .363 .366
17 8003 5631 85 156 7918 5475 9944 6595 90 168 9859 6439 0 0 4002 2734 33 88 98 100 98 100 13393 16298 1.446 .691 .653 1.113 .714 2.522 52 289 .675 .98 80 4190 19400 80 88 333 341 0 7609 211 7399 .934 8912 8701 1.07 .883 -.098 -.18
18 995 941 84 153 911 788 1006 924 90 159 922 771 0 0 253 212 40 60 100 100 100 100 1699 1693 1.156 .865 .836 .915 .864 .309 52 352 .781 .92 90 4350 19400 79 88 348 357 0 1272 207 1065 1.169 1249 1042 .856 1.13 .225 .176
19 1887 2101 93 168 1794 1933 1903 2071 96 176 1810 1903 0 0 404 436 28 65 100 100 100 100 3727 3713 .928 1.077 1.051 1.105 1.042 .243 52 346 1.011 .96 90 4510 19400 79 88 364 373 0 2839 227 2612 1.456 2799 2572 .687 1.421 .542 .507
20 3459 3594 87 164 3372 3430 3606 3844 91 170 3519 3680 0 0 2102 2208 28 61 97 100 97 97 6802 7199 .983 1.017 1.046 1.381 1.03 1.808 80 419 1.006 .98 100 4670 19400 79 89 380 390 0 4857 222 4635 1.375 5195 4973 .727 1.413 .459 .499

Total number of rows: 21888

Table truncated, full table size 4891 Kbytes.




Supplementary data files not provided
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