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Sample GSM64245 Query DataSets for GSM64245
Status Public on Jul 16, 2005
Title GSY7-A
Sample type genomic
 
Channel 1
Source name S288C sonicated genomic DNA 4 ug
Organism Saccharomyces cerevisiae
Characteristics S288C sonicated genomic DNA 4 ug
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name GSY7 sonicated genomic DNA 4 ug
Organism Saccharomyces cerevisiae
Characteristics GSY7 sonicated genomic DNA 4 ug
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48283.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 15, 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 GPL2634
Series (1)
GSE2949 CommercialWineYeastStrainsCGH

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 1062 743 176 110 886 633 823 601 178 113 647 491 0 0 610 421 36 35 100 100 100 100 1519 1138 1.4 .714 .759 .722 .73 1.316 52 340 .699 .958 80 1680 8230 51 59 40 48 0 1026 152 874 .987 830 678 1.013 1.048 -.019 .068
2 1614 872 169 110 1445 762 1371 709 175 113 1202 599 0 0 817 438 41 35 100 100 100 100 2207 1801 1.896 .527 .498 .522 .521 1.351 80 568 .523 .938 110 1870 8230 49 60 57 68 0 1205 152 1053 .728 979 827 1.373 .688 -.457 -.539
3 701 805 170 105 531 700 709 817 173 109 539 712 0 0 153 195 34 31 100 100 100 100 1231 1251 .759 1.318 1.321 1.317 1.314 1.262 80 554 1.328 .92 110 2050 8220 48 59 75 86 0 1112 145 967 1.821 1129 984 .549 1.825 .865 .868
4 1254 1225 170 107 1084 1118 1275 1265 174 112 1105 1158 0 0 268 274 37 37 100 100 100 100 2202 2263 .97 1.031 1.048 1.033 1.022 1.181 80 541 1.027 .954 110 2230 8220 48 59 93 104 0 1692 148 1544 1.425 1747 1600 .702 1.448 .511 .534
5 1689 937 169 106 1520 831 1796 1017 173 110 1627 911 0 0 420 244 38 36 99 100 99 99 2351 2538 1.829 .547 .56 .549 .559 1.339 120 630 .543 .95 120 2420 8230 49 61 112 124 0 1294 146 1148 .755 1405 1258 1.324 .773 -.405 -.371
6 720 314 166 106 554 208 597 270 169 109 431 164 0 0 388 153 30 30 100 93 98 83 762 595 2.663 .375 .381 .368 .365 1.569 80 457 .367 .862 100 2600 8220 49 59 131 141 0 434 146 287 .519 373 227 1.928 .526 -.947 -.928
7 1177 451 165 103 1012 348 1095 438 168 104 930 335 0 0 414 159 34 28 100 100 100 100 1360 1265 2.908 .344 .36 .336 .36 1.367 80 464 .34 .886 100 2780 8230 50 60 149 159 0 623 142 481 .475 605 463 2.105 .498 -1.074 -1.007
8 1307 589 163 103 1144 486 1249 505 167 105 1086 402 0 0 734 328 34 27 100 100 100 97 1630 1488 2.354 .425 .37 .415 .418 1.421 80 546 .426 .944 110 2960 8220 48 59 166 177 0 814 142 671 .587 698 555 1.704 .511 -.769 -.968
9 935 586 164 100 771 486 714 462 168 103 550 362 0 0 525 323 34 28 100 100 100 100 1257 912 1.586 .63 .658 .634 .621 1.336 80 558 .617 .931 110 3140 8220 48 59 184 195 0 809 138 671 .871 638 500 1.148 .909 -.2 -.137
10 608 678 166 104 442 574 542 610 171 107 376 506 0 0 202 257 35 28 100 100 100 100 1016 882 .77 1.299 1.346 1.306 1.301 1.29 80 548 1.297 .916 110 3330 8230 49 60 203 214 0 937 144 793 1.794 843 699 .557 1.859 .843 .894
11 293 228 166 102 127 126 268 203 174 118 102 101 0 0 110 100 57 147 69 26 40 11 253 203 1.008 .992 .99 .934 1.01 1.887 52 379 2.431 .577 90 3510 8230 50 59 222 231 0 315 141 174 1.37 280 140 .73 1.368 .455 .452
12 2033 801 167 104 1866 697 2337 850 172 115 2170 746 0 0 797 298 53 133 100 98 98 90 2563 2916 2.677 .374 .344 .384 .381 1.32 80 472 .36 .93 100 3690 8230 50 60 240 250 0 1106 144 963 .516 1174 1030 1.938 .475 -.955 -1.074
13 1154 530 170 111 984 419 957 436 172 113 787 325 0 0 520 247 40 34 100 100 100 98 1403 1112 2.348 .426 .413 .413 .43 1.401 80 485 .431 .923 100 3880 8220 49 59 259 269 0 732 153 579 .588 602 449 1.7 .57 -.766 -.81
14 551 577 169 107 382 470 551 572 172 110 382 465 0 0 129 130 37 30 100 100 100 100 852 847 .813 1.23 1.217 1.25 1.257 1.274 80 516 1.207 .893 110 4060 8220 48 59 276 287 0 797 148 649 1.7 790 642 .588 1.681 .765 .75
15 1994 1069 167 103 1827 966 2112 1152 169 107 1945 1049 0 0 627 353 34 29 99 100 99 100 2793 2994 1.891 .529 .539 .544 .53 1.628 120 582 .526 .959 120 4240 8220 48 60 294 306 0 1477 142 1334 .73 1591 1449 1.369 .745 -.453 -.425
16 1604 869 165 101 1439 768 1404 727 186 124 1239 626 0 0 838 462 147 173 100 100 100 83 2207 1865 1.874 .534 .505 .534 .527 1.251 80 510 .536 .897 110 4420 8220 48 59 312 323 0 1200 140 1061 .737 1004 865 1.356 .698 -.44 -.519
17 833 713 166 106 667 607 680 578 184 126 514 472 0 0 430 396 139 163 94 93 85 70 1274 986 1.099 .91 .918 .916 .915 1.419 120 571 .912 .938 120 4610 8220 48 60 331 343 0 985 146 838 1.257 798 652 .795 1.268 .33 .343
18 1244 899 164 104 1080 795 1279 884 168 106 1115 780 0 0 344 248 32 27 100 100 99 100 1875 1895 1.358 .736 .7 .749 .732 1.303 120 560 .728 .948 120 4790 8220 48 60 349 361 0 1242 144 1098 1.017 1221 1077 .983 .966 .024 -.049
19 2419 854 162 99 2257 755 2332 784 166 103 2170 685 0 0 885 331 32 26 100 100 100 100 3012 2855 2.989 .335 .316 .326 .318 1.361 80 458 .329 .925 100 4970 8220 49 59 368 378 0 1180 137 1043 .462 1083 946 2.164 .436 -1.114 -1.197
20 380 219 161 98 219 121 388 212 165 101 227 114 0 0 107 52 30 27 98 100 92 86 340 341 1.81 .553 .502 .59 .527 1.819 52 308 .501 .644 80 5150 8210 49 57 387 395 0 303 135 167 .763 293 157 1.31 .694 -.39 -.528

Total number of rows: 7056

Table truncated, full table size 1582 Kbytes.




Supplementary data files not provided
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