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Sample GSM87480 Query DataSets for GSM87480
Status Public on Dec 15, 2005
Title DBY8778_heat_shock2_60min
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, 60 min after transfer from 25 to37C
Organism Saccharomyces cerevisiae
Characteristics DBY8778, 60 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/2002-08/32255.gif
Measurement: time(absolute) 60 m
name: 32255_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 9552 9707 85 138 9467 9569 10024 10339 104 162 9939 10201 0 0 2785 3411 141 105 100 100 100 100 19036 20140 .989 1.011 1.026 .983 1.01 1.35 120 692 1.036 .96 130 1750 9430 88 101 52 65 0 11287 160 11127 1.175 12022 11862 .851 1.193 .233 .255
2 2493 1147 77 126 2416 1021 2581 1070 96 153 2504 944 0 0 1141 553 142 107 98 99 96 96 3437 3448 2.366 .423 .377 .43 .405 1.608 156 664 .404 .91 140 1930 9430 88 102 70 84 0 1334 147 1187 .491 1244 1098 2.035 .438 -1.025 -1.19
3 736 665 89 157 647 508 765 679 103 187 676 522 0 0 236 252 55 130 97 92 95 83 1155 1198 1.274 .785 .772 .712 .74 1.671 120 561 .877 .88 130 2120 9430 88 101 89 102 0 773 183 591 .913 790 607 1.095 .898 -.131 -.155
4 5716 5312 94 160 5622 5152 6203 5344 112 199 6109 5184 0 0 1930 1566 60 141 100 100 100 100 10774 11293 1.091 .916 .849 .975 .888 1.546 156 662 .888 .94 140 2300 9430 88 102 107 121 0 6177 186 5991 1.066 6214 6028 .938 .987 .092 -.019
5 766 487 88 144 678 343 796 480 106 177 708 336 0 0 199 139 57 122 100 95 99 77 1021 1044 1.977 .506 .475 .498 .513 1.367 120 563 .523 .8 130 2480 9430 88 101 125 138 0 566 167 399 .588 558 391 1.7 .552 -.765 -.858
6 3436 2527 94 146 3342 2381 3627 2575 138 182 3533 2429 0 0 1033 838 194 145 100 100 100 99 5723 5962 1.404 .712 .688 .711 .695 1.334 120 671 .69 .94 130 2660 9430 88 101 143 156 0 2938 170 2769 .828 2994 2824 1.207 .799 -.272 -.323
7 391 538 146 191 245 347 338 435 175 218 192 244 0 0 189 324 106 132 78 71 44 44 592 436 .706 1.416 1.271 1.284 1.376 2.278 52 269 1.624 .79 80 2860 9390 87 95 166 174 0 626 222 403 1.647 506 284 .607 1.478 .72 .563
8 10536 5333 99 153 10437 5180 11019 5564 139 185 10920 5411 0 0 3496 1626 173 129 100 100 100 100 15617 16331 2.015 .496 .496 .508 .479 1.345 120 623 .46 .95 130 3030 9430 88 101 180 193 0 6201 178 6023 .577 6470 6292 1.733 .576 -.793 -.795
9 2443 3559 85 120 2358 3439 2568 3767 115 153 2483 3647 0 0 738 1288 167 118 100 99 98 98 5797 6130 .686 1.458 1.469 1.382 1.479 1.735 156 610 1.552 .93 140 3220 9440 89 103 199 213 0 4138 140 3999 1.696 4380 4241 .59 1.708 .762 .772
10 785 929 82 103 703 826 791 871 99 128 709 768 0 0 228 308 57 84 100 100 97 100 1529 1477 .851 1.175 1.083 1.186 1.131 1.405 120 574 1.174 .92 130 3390 9430 88 101 216 229 0 1080 120 960 1.366 1013 893 .732 1.26 .45 .333
11 1846 1527 79 97 1767 1430 1997 1568 96 121 1918 1471 0 0 474 409 56 84 100 100 100 100 3197 3389 1.236 .809 .767 .824 .811 1.304 120 622 .796 .96 130 3580 9430 88 101 235 248 0 1776 113 1663 .941 1823 1710 1.063 .892 -.088 -.165
12 388 330 76 95 312 235 399 331 99 126 323 236 0 0 99 103 76 100 96 90 93 65 547 559 1.328 .753 .731 .706 .737 1.558 120 584 .82 .84 130 3760 9430 88 101 253 266 0 384 110 273 .876 385 274 1.142 .85 -.191 -.235
13 1065 1074 79 100 986 974 1155 1110 108 137 1076 1010 0 0 381 440 84 109 100 100 96 94 1960 2086 1.012 .988 .939 .962 .999 1.403 156 639 1.023 .95 140 3940 9430 88 102 271 285 0 1249 116 1133 1.149 1291 1174 .871 1.091 .2 .126
14 1974 2913 96 126 1878 2787 2072 2963 135 164 1976 2837 0 0 700 996 115 134 98 100 98 98 4665 4813 .674 1.484 1.436 1.513 1.448 1.345 156 622 1.491 .97 140 4120 9430 88 102 289 303 0 3387 147 3241 1.726 3445 3299 .58 1.669 .787 .739
15 9165 2461 95 129 9070 2332 8535 2226 133 165 8440 2097 0 0 4127 1285 112 129 100 98 100 97 11402 10537 3.889 .257 .248 .246 .242 1.587 156 630 .249 .91 140 4310 9430 88 102 308 322 0 2862 150 2712 .299 2588 2438 3.345 .289 -1.742 -1.791
16 3070 5032 75 97 2995 4935 3325 4943 97 124 3250 4846 0 0 1068 1725 63 88 100 100 100 100 7930 8096 .607 1.648 1.491 1.722 1.616 1.478 156 605 1.676 .96 140 4490 9430 88 102 326 340 0 5851 113 5738 1.916 5748 5635 .522 1.734 .938 .794
17 819 676 70 82 749 594 933 701 84 100 863 619 0 0 330 236 46 61 97 100 96 100 1343 1482 1.261 .793 .717 .857 .761 1.693 156 585 .761 .94 140 4670 9430 88 102 344 358 0 786 95 691 .922 815 720 1.084 .834 -.117 -.262
18 1573 1549 70 84 1503 1465 1670 1634 84 95 1600 1550 0 0 533 555 43 49 100 100 99 100 2968 3150 1.026 .975 .969 .969 .978 1.288 156 614 .984 .97 140 4850 9430 88 102 362 376 0 1801 98 1703 1.133 1900 1802 .882 1.126 .181 .172
19 723 582 71 78 652 504 719 487 84 87 648 409 0 0 216 267 42 44 100 100 100 98 1156 1057 1.294 .773 .631 .709 .73 1.524 120 570 .83 .91 130 5030 9420 87 100 380 393 0 677 91 586 .899 566 476 1.113 .734 -.154 -.446
20 448 448 71 75 377 373 485 467 83 86 414 392 0 0 182 195 42 43 92 91 89 88 750 806 1.011 .989 .947 .927 1 1.793 156 640 1.011 .92 140 5220 9430 88 102 399 413 0 521 87 434 1.15 543 456 .869 1.101 .202 .139

Total number of rows: 13824

Table truncated, full table size 2943 Kbytes.




Supplementary data files not provided
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