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Sample GSM87481 Query DataSets for GSM87481
Status Public on Dec 15, 2005
Title delKIN82_heat shock _0min_repeat
Sample type RNA
 
Channel 1
Source name delKIN82, mid-log (0.22 OD) @ 30C
Organism Saccharomyces cerevisiae
Characteristics delKIN82, mid-log (0.22 OD) @ 30C
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name delKIN82, 0min after transfer from 25C to 37C
Organism Saccharomyces cerevisiae
Characteristics delKIN82, 0min after transfer from 25C to 37C
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-09/33414.gif
Measurement: time(absolute) 0 m
name: 33414_Time
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 Dec 13, 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 GPL2637
Series (1)
GSE3812 Response of yeast cells to stress

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 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
1 6868 10065 62 147 6806 9918 7601 10462 78 165 7539 10315 0 0 2634 3055 44 82 99 100 99 100 16724 17854 .686 1.457 1.368 1.579 1.399 1.691 156 818 1.433 .95 140 2120 8610 74 88 57 71 0 12426 181 12244 1.799 12916 12735 .556 1.689 .847 .756
2 1171 1596 62 135 1109 1461 1145 1497 74 143 1083 1362 0 0 298 565 33 53 100 100 100 100 2570 2445 .759 1.317 1.258 1.276 1.253 1.31 120 579 1.495 .92 130 2290 8600 73 86 74 87 0 1970 167 1804 1.626 1848 1681 .615 1.553 .702 .635
3 397 413 64 129 333 284 418 404 76 135 354 275 0 0 109 117 34 47 99 98 99 96 617 629 1.173 .853 .777 .829 .815 1.614 120 591 .899 .85 130 2480 8610 74 87 93 106 0 510 159 351 1.053 499 340 .95 .959 .074 -.06
4 6391 6637 67 135 6324 6502 7027 7046 79 139 6960 6911 0 0 2232 1892 37 48 100 100 99 100 12826 13871 .973 1.028 .993 1.103 .988 1.666 156 651 1.001 .96 140 2660 8610 74 88 111 125 0 8194 167 8027 1.269 8699 8532 .788 1.226 .344 .294
5 596 660 66 142 530 518 574 672 80 145 508 530 0 0 165 180 39 47 100 99 100 99 1048 1038 1.023 .977 1.043 .952 .952 1.382 120 540 1.022 .93 130 2850 8600 73 86 130 143 0 815 175 640 1.207 830 654 .829 1.288 .271 .365
6 584 929 66 136 518 793 615 929 80 142 549 793 0 0 224 247 40 50 95 100 95 100 1311 1342 .653 1.531 1.444 1.566 1.443 1.518 156 687 1.511 .91 140 3020 8610 74 88 147 161 0 1147 168 979 1.89 1147 979 .529 1.783 .918 .835
7 209 200 63 126 146 74 193 198 76 129 130 72 0 0 63 57 39 39 100 70 91 46 220 202 1.973 .507 .554 .407 .529 2.874 120 591 .521 .56 130 3210 8600 73 86 166 179 0 247 156 91 .626 244 89 1.598 .684 -.676 -.548
8 2894 2548 63 126 2831 2422 3240 2793 78 130 3177 2667 0 0 1080 837 40 42 100 100 99 99 5253 5844 1.169 .856 .839 .877 .847 1.376 156 662 .839 .95 140 3390 8600 73 87 184 198 0 3146 156 2990 1.056 3448 3293 .947 1.036 .079 .052
9 1687 2818 64 120 1623 2698 1753 2869 89 142 1689 2749 0 0 377 591 108 150 100 100 100 100 4321 4438 .602 1.662 1.628 1.668 1.673 1.198 120 597 1.74 .96 130 3570 8600 73 86 202 215 0 3479 148 3331 2.052 3542 3394 .487 2.009 1.037 1.007
10 527 551 65 112 462 439 553 562 100 147 488 450 0 0 207 214 143 213 93 83 79 57 901 938 1.052 .95 .922 .977 1.008 2.111 120 580 1.001 .89 130 3760 8610 74 87 221 234 0 680 138 542 1.173 694 556 .852 1.138 .23 .187
11 768 1001 62 105 706 896 751 1041 79 109 689 936 0 0 307 352 45 42 100 100 99 100 1602 1625 .788 1.269 1.358 1.297 1.222 1.368 120 512 1.275 .94 120 3930 8600 74 86 239 251 0 1236 130 1106 1.567 1285 1156 .638 1.677 .648 .746
12 293 339 62 104 231 235 292 334 79 108 230 230 0 0 93 89 49 43 98 97 90 95 466 460 .983 1.017 1 1.05 1.016 1.825 120 545 1.069 .81 120 4120 8610 75 87 258 270 0 419 128 290 1.256 412 284 .796 1.235 .329 .304
13 687 946 64 107 623 839 719 995 89 111 655 888 0 0 214 283 94 50 98 100 96 100 1462 1543 .743 1.347 1.356 1.36 1.348 1.387 120 550 1.372 .91 120 4300 8600 74 86 276 288 0 1168 132 1036 1.663 1228 1096 .601 1.674 .733 .743
14 552 931 69 116 483 815 575 953 105 131 506 837 0 0 259 364 108 80 87 96 80 92 1298 1343 .593 1.687 1.654 1.74 1.519 2.195 156 681 1.772 .85 140 4490 8610 74 88 294 308 0 1149 143 1006 2.083 1177 1033 .48 2.042 1.059 1.03
15 7198 9840 65 118 7133 9722 7911 10517 94 136 7846 10399 0 0 2582 3336 81 80 100 100 100 100 16855 18245 .734 1.363 1.325 1.367 1.33 1.29 156 675 1.373 .96 140 4660 8600 73 87 311 325 0 12148 146 12002 1.683 12984 12838 .594 1.636 .751 .71
16 1769 2119 68 111 1701 2008 1813 2115 84 126 1745 2004 0 0 312 332 50 78 100 100 100 100 3709 3749 .847 1.18 1.148 1.186 1.194 1.193 120 612 1.201 .96 130 4840 8600 73 86 329 342 0 2616 137 2479 1.457 2611 2474 .686 1.418 .543 .504
17 606 534 66 109 540 425 624 528 81 114 558 419 0 0 203 164 43 41 100 100 100 99 965 977 1.271 .787 .751 .783 .786 1.447 120 603 .791 .93 130 5020 8610 74 87 347 360 0 659 135 525 .972 652 517 1.029 .927 -.041 -.109
18 1173 1328 64 109 1109 1219 1228 1358 77 117 1164 1249 0 0 330 351 38 53 99 100 99 100 2328 2413 .91 1.099 1.073 1.113 1.065 1.405 120 615 1.14 .93 130 5210 8600 73 86 366 379 0 1640 135 1505 1.357 1677 1542 .737 1.325 .44 .406
19 436 373 64 112 372 261 440 369 78 116 376 257 0 0 102 96 38 41 100 100 100 98 633 633 1.425 .702 .684 .675 .684 1.494 120 621 .729 .88 130 5390 8600 73 86 384 397 0 460 138 322 .866 456 317 1.154 .844 -.207 -.245
20 261 241 66 103 195 138 265 247 79 107 199 144 0 0 112 85 41 39 85 87 83 76 333 343 1.413 .708 .724 .735 .685 2.357 80 473 .653 .77 110 5570 8590 73 84 403 414 0 298 127 170 .874 305 178 1.145 .893 -.195 -.163

Total number of rows: 13824

Table truncated, full table size 2956 Kbytes.




Supplementary data files not provided
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