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Sample GSM64255 Query DataSets for GSM64255
Status Public on Jul 16, 2005
Title GSY2A
Sample type genomic
 
Channel 1
Source name S288C sonicated genomic DNA 4ug
Organism Saccharomyces cerevisiae
Characteristics S288C sonicated genomic DNA 4ug
Extracted molecule genomic DNA
Label Cy3
 
Channel 2
Source name GSY2 sonicated DNA 4 ug
Organism Saccharomyces cerevisiae
Characteristics GSY2 sonicated DNA 4 ug
Extracted molecule genomic DNA
Label Cy5
 
 
Description Simple annotation: Wine, DNA
Image: http://smd.stanford.edu/MicroArray/gifs/2004-01/48031.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 (2)
GSE2949 CommercialWineYeastStrainsCGH
GSE23055 Karyotyping of maltose-fermenting Saccharomyces yeasts with differing maltotriose utilization profiles

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 4274 3398 445 160 3829 3238 4105 2940 455 175 3660 2780 0 0 1767 1555 95 91 100 100 100 100 7067 6440 1.183 .846 .76 .844 .872 1.398 52 327 .842 .926 80 1900 8580 58 66 46 54 0 4130 194 3935 1.028 3573 3379 .973 .923 .039 -.115
2 5721 4549 447 152 5274 4397 5077 3874 456 164 4630 3722 0 0 2319 2050 81 80 100 100 100 100 9671 8352 1.199 .834 .804 .829 .838 1.255 80 551 .84 .926 110 2100 8570 55 66 64 75 0 5528 185 5344 1.013 4708 4523 .987 .977 .019 -.034
3 3611 2876 452 155 3159 2721 3703 2895 457 161 3251 2740 0 0 550 270 63 54 100 100 100 100 5880 5991 1.161 .861 .843 .887 .853 1.347 120 674 .835 .938 130 2280 8580 55 68 81 94 0 3495 188 3307 1.047 3518 3330 .955 1.024 .066 .035
4 4511 4195 463 162 4048 4033 4635 4222 470 167 4172 4060 0 0 729 479 76 55 100 100 100 100 8081 8232 1.004 .996 .973 1.022 .992 1.317 120 648 .975 .943 130 2460 8580 55 68 99 112 0 5098 197 4901 1.211 5131 4934 .826 1.183 .276 .242
5 4678 3821 464 167 4214 3654 4723 3835 486 179 4259 3668 0 0 613 573 132 90 100 100 100 100 7868 7927 1.153 .867 .861 .869 .87 1.252 120 664 .865 .944 130 2650 8580 55 68 118 131 0 4644 203 4441 1.054 4661 4458 .949 1.047 .076 .066
6 2545 2056 464 165 2081 1891 1725 1417 506 187 1261 1252 0 0 1685 1521 629 245 78 100 50 80 3972 2513 1.1 .909 .993 .905 .929 1.552 80 484 .78 .828 110 2830 8580 56 67 137 148 0 2499 201 2298 1.104 1722 1522 .906 1.207 .143 .271
7 2158 1852 474 166 1684 1686 2187 1860 490 174 1713 1694 0 0 246 273 174 64 100 100 99 100 3370 3407 .999 1.001 .989 1.002 .989 1.26 120 550 1.005 .921 120 3010 8580 56 68 155 167 0 2251 202 2049 1.217 2260 2059 .822 1.202 .283 .265
8 4135 3507 474 166 3661 3341 3293 2763 483 176 2819 2597 0 0 2054 1873 75 60 99 100 99 100 7002 5416 1.096 .913 .921 .927 .933 1.467 120 572 .91 .925 120 3190 8580 56 68 173 185 0 4262 202 4060 1.109 3358 3156 .902 1.12 .149 .163
9 3325 2739 473 159 2852 2580 3255 2537 478 164 2782 2378 0 0 948 887 73 54 99 100 99 100 5432 5160 1.105 .905 .855 .929 .889 1.54 120 558 .902 .919 120 3380 8580 56 68 192 204 0 3329 193 3135 1.099 3083 2890 .91 1.039 .137 .055
10 3272 2817 457 162 2815 2655 3311 2796 466 167 2854 2634 0 0 835 692 92 52 99 100 97 100 5470 5488 1.06 .943 .923 .999 .932 1.671 120 557 .927 .924 120 3560 8580 56 68 210 222 0 3423 197 3227 1.146 3398 3201 .872 1.122 .197 .166
11 1320 785 462 156 858 629 1066 542 465 161 604 386 0 0 744 591 72 55 100 98 97 97 1487 990 1.364 .733 .639 .731 .785 1.711 80 490 .739 .85 110 3740 8570 55 66 228 239 -100 954 190 764 .891 659 469 1.122 .777 -.167 -.365
12 3099 2547 465 155 2634 2392 2924 2304 469 162 2459 2149 0 0 1267 1178 66 55 100 100 99 100 5026 4608 1.101 .908 .874 .911 .922 1.517 120 555 .906 .932 120 3920 8580 56 68 246 258 0 3095 188 2907 1.104 2800 2612 .906 1.062 .142 .087
13 2605 2283 467 157 2138 2126 2603 2287 469 165 2136 2130 0 0 452 378 73 57 100 100 99 100 4264 4266 1.006 .994 .997 1.02 .979 1.398 120 567 .978 .931 120 4100 8580 56 68 264 276 0 2775 191 2584 1.208 2779 2589 .827 1.212 .273 .277
14 3717 2862 476 167 3241 2695 3638 2774 493 182 3162 2607 0 0 707 678 129 103 100 100 100 100 5936 5769 1.203 .832 .824 .825 .83 1.189 120 551 .835 .957 120 4290 8580 56 68 283 295 0 3478 203 3275 1.011 3371 3168 .99 1.002 .015 .003
15 5600 5332 490 164 5110 5168 5680 5387 506 187 5190 5223 0 0 844 977 167 157 100 100 100 100 10278 10413 .989 1.011 1.006 1.006 1.017 1.156 120 598 1.011 .957 130 4460 8580 55 68 299 312 0 6480 199 6281 1.229 6547 6347 .814 1.223 .298 .29
16 4162 3735 493 164 3669 3571 3967 3512 875 243 3474 3348 0 0 1263 1342 3825 571 40 100 0 100 7240 6822 1.027 .973 .964 .968 .967 1.272 120 545 .983 .917 120 4650 8580 56 68 319 331 0 4539 199 4340 1.183 4268 4069 .845 1.171 .242 .228
17 5096 4233 494 173 4602 4060 5240 4128 966 316 4746 3955 0 0 1033 1130 4032 1020 67 100 0 98 8662 8701 1.133 .882 .833 .87 .89 1.183 120 524 .891 .96 120 4830 8580 56 68 337 349 0 5144 210 4934 1.072 5017 4806 .933 1.013 .101 .018
18 9775 9216 472 168 9303 9048 9220 9075 514 208 8748 8907 0 0 3926 3040 273 298 99 100 99 100 18351 17655 1.028 .973 1.018 1.022 .985 1.436 120 568 .916 .922 120 5010 8580 56 68 355 367 0 11200 204 10996 1.182 11029 10825 .846 1.237 .241 .307
19 5497 4496 470 167 5027 4329 5698 4577 515 212 5228 4410 0 0 1382 1392 310 309 100 98 98 98 9356 9638 1.161 .861 .844 .816 .867 1.536 120 585 .869 .941 120 5200 8580 56 68 374 386 0 5464 203 5261 1.047 5562 5359 .956 1.025 .066 .036
20 1320 928 456 171 864 757 1396 1000 473 187 940 829 0 0 420 331 108 91 98 100 90 92 1621 1769 1.141 .876 .882 .891 .854 1.477 52 297 .829 .867 80 5360 8570 57 65 392 400 0 1128 208 920 1.065 1215 1007 .939 1.072 .091 .1

Total number of rows: 7056

Table truncated, full table size 1641 Kbytes.




Supplementary data files not provided
Processed data included within Sample table
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