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Sample GSM87476 Query DataSets for GSM87476
Status Public on Dec 15, 2005
Title DBY8778_heat_shock2_5min
Sample type RNA
 
Channel 1
Source name DBY8778, mid-log (0.4 OD) @ 30C
Organism Saccharomyces cerevisiae
Characteristics DBY8778, mid-log (0.4 OD) @ 30C
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name DBY8778, 5 min after transfer from 25 to37C
Organism Saccharomyces cerevisiae
Characteristics DBY8778, 5 min after transfer from 25 to37C
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, heat shock
Image: http://smd.stanford.edu/MicroArray/gifs/2002-08/32251.gif
Measurement: time(absolute) 5 m
name: 32251_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 17458 9615 139 229 17319 9386 18854 10050 172 286 18715 9821 0 0 6842 4359 112 207 100 100 100 99 26705 28536 1.845 .542 .525 .512 .526 1.469 156 773 .549 .96 140 1740 9320 117 131 59 73 0 11052 263 10789 .623 11552 11289 1.605 .603 -.683 -.729
2 4756 1535 143 229 4613 1306 4465 1345 185 290 4322 1116 0 0 2109 766 134 220 100 97 100 91 5919 5438 3.532 .283 .258 .267 .272 1.494 156 609 .285 .92 140 1920 9320 117 131 77 91 0 1764 263 1501 .325 1546 1283 3.073 .297 -1.62 -1.752
3 1293 1180 165 271 1128 909 1244 1025 218 336 1079 754 0 0 468 576 161 245 99 93 94 79 2037 1833 1.241 .806 .699 .71 .77 1.73 120 486 .938 .89 120 2100 9310 117 129 96 108 0 1356 311 1045 .926 1178 867 1.08 .803 -.111 -.316
4 12696 6006 149 240 12547 5766 12758 5610 198 301 12609 5370 0 0 4608 2479 146 217 100 100 100 100 18313 17979 2.176 .46 .426 .458 .444 1.323 156 628 .462 .97 140 2280 9320 117 131 113 127 0 6903 276 6628 .528 6448 6172 1.893 .49 -.921 -1.031
5 1380 986 129 187 1251 799 1400 906 175 239 1271 719 0 0 535 428 129 177 97 94 96 88 2050 1990 1.566 .639 .566 .585 .593 1.766 120 534 .665 .9 130 2460 9320 117 130 131 144 0 1133 215 918 .734 1041 826 1.362 .65 -.446 -.621
6 3667 3145 123 157 3544 2988 4065 3336 169 207 3942 3179 0 0 1416 1214 131 161 98 98 98 97 6532 7121 1.186 .843 .806 .838 .845 1.519 156 666 .835 .95 140 2640 9320 117 131 149 163 0 3615 180 3434 .969 3834 3654 1.032 .927 -.045 -.109
7 557 442 125 151 432 291 564 399 173 210 439 248 0 0 186 184 140 171 91 77 81 32 723 687 1.485 .674 .565 .626 .655 1.825 120 594 .823 .7 130 2830 9310 116 129 168 181 0 508 174 334 .774 459 285 1.292 .649 -.369 -.623
8 14103 2744 116 141 13987 2603 15166 2847 157 185 15050 2706 0 0 4756 984 123 147 100 100 100 99 16590 17756 5.373 .186 .18 .187 .187 1.483 156 634 .179 .96 140 3010 9320 117 131 186 200 0 3154 162 2992 .214 3272 3110 4.675 .207 -2.225 -2.275
9 2863 4342 104 140 2759 4202 3063 4337 131 171 2959 4197 0 0 968 1789 86 109 100 99 100 97 6961 7156 .657 1.523 1.418 1.407 1.494 1.86 156 552 1.639 .93 140 3190 9330 118 132 204 218 0 4991 161 4830 1.751 4985 4824 .571 1.63 .808 .705
10 1207 1337 97 137 1110 1200 1282 1324 120 166 1185 1187 0 0 427 565 75 117 100 100 98 97 2310 2372 .925 1.081 1.002 1.066 1.013 1.586 156 593 1.155 .88 140 3370 9320 117 131 222 236 0 1537 157 1379 1.243 1522 1364 .805 1.151 .313 .203
11 2002 2010 98 133 1904 1877 2214 2149 123 161 2116 2016 0 0 687 779 84 110 100 99 99 98 3781 4132 1.014 .986 .953 .954 1.005 1.59 156 617 1.015 .95 140 3560 9320 117 131 241 255 0 2310 153 2157 1.133 2470 2317 .883 1.095 .18 .131
12 473 720 101 133 372 587 498 734 129 165 397 601 0 0 150 278 88 103 91 92 86 88 959 998 .634 1.578 1.514 1.476 1.568 2.061 156 636 1.77 .83 140 3740 9320 117 131 259 273 0 828 153 675 1.814 844 691 .551 1.74 .859 .799
13 1094 1229 108 134 986 1095 1111 1232 141 165 1003 1098 0 0 409 446 115 100 95 99 90 98 2081 2101 .9 1.111 1.095 1.177 1.106 1.86 120 586 1.094 .87 130 3930 9320 117 130 278 291 0 1413 154 1259 1.276 1416 1262 .783 1.258 .352 .331
14 1722 2416 112 133 1610 2283 1920 2497 160 166 1808 2364 0 0 792 1308 154 118 90 96 87 94 3893 4172 .705 1.418 1.308 1.346 1.347 1.86 156 705 1.532 .92 140 4110 9320 117 131 296 310 0 2777 153 2624 1.63 2870 2717 .614 1.503 .705 .588
15 16588 1506 103 133 16485 1373 16328 1530 153 163 16225 1397 0 0 4337 427 138 113 100 100 100 98 17858 17622 12.007 .083 .086 .082 .085 1.323 156 655 .078 .94 140 4300 9320 117 131 315 329 0 1731 153 1578 .096 1759 1606 10.446 .099 -3.385 -3.337
16 2358 7864 98 141 2260 7723 2529 8171 136 173 2431 8030 0 0 678 2550 112 119 98 100 97 100 9983 10461 .293 3.417 3.303 3.492 3.425 1.494 156 652 3.598 .97 140 4480 9320 117 131 333 347 0 9039 162 8877 3.928 9392 9230 .255 3.797 1.974 1.925
17 867 680 88 136 779 544 893 710 115 173 805 574 0 0 340 269 81 124 95 92 92 85 1323 1379 1.432 .698 .713 .672 .692 1.591 120 552 .715 .88 130 4670 9330 118 131 352 365 0 782 156 625 .803 816 660 1.246 .82 -.317 -.287
18 1746 2492 87 130 1659 2362 1927 2499 108 156 1840 2369 0 0 602 852 64 97 98 100 94 99 4021 4209 .702 1.424 1.288 1.524 1.369 1.479 120 585 1.415 .94 130 4850 9320 117 130 370 383 0 2864 149 2715 1.636 2872 2723 .611 1.48 .711 .565
19 738 522 79 114 659 408 757 501 100 133 678 387 0 0 260 208 60 78 98 96 97 90 1067 1065 1.615 .619 .571 .601 .584 1.636 156 641 .647 .91 140 5040 9320 117 131 389 403 0 600 131 469 .712 576 445 1.405 .656 -.491 -.608
20 678 649 79 112 599 537 736 682 104 125 657 570 0 0 239 236 63 66 95 95 91 92 1136 1227 1.115 .896 .868 .929 .912 1.64 120 581 .927 .92 130 5210 9320 117 130 406 419 0 746 129 617 1.03 784 655 .97 .997 .043 -.004

Total number of rows: 13824

Table truncated, full table size 3013 Kbytes.




Supplementary data files not provided
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