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Sample GSM87493 Query DataSets for GSM87493
Status Public on Dec 15, 2005
Title delYPL230w_stationary_phase_1day
Sample type RNA
 
Channel 1
Source name delYPL230w, mid-log phase @ 30C (0.37 OD)
Organism Saccharomyces cerevisiae
Characteristics delYPL230w, mid-log phase @ 30C (0.37 OD)
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name delYPL230w, stationary phase 15.6 OD (1 day)
Organism Saccharomyces cerevisiae
Characteristics delYPL230w, stationary phase 15.6 OD (1 day)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, YPD-stationary-phase
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33782.gif
Measurement: time(absolute) 20 h
name: 33782_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 3125 1671 47 63 3078 1608 3261 1661 49 65 3214 1598 0 0 1387 906 11 26 99 95 99 94 4686 4812 1.914 .522 .497 .504 .485 2.646 156 804 .5 .84 140 1710 9190 100 114 80 94 0 2228 84 2144 .697 2215 2131 1.436 .663 -.522 -.593
2 1214 328 47 63 1167 265 1165 314 48 67 1118 251 0 0 337 136 10 27 100 99 100 97 1432 1369 4.404 .227 .225 .21 .216 1.727 120 593 .209 .79 130 1900 9190 100 113 99 112 0 437 84 353 .303 419 335 3.303 .299 -1.724 -1.74
3 190 226 47 63 143 163 195 213 53 68 148 150 0 0 45 89 72 28 93 96 50 92 306 298 .877 1.14 1.014 1.014 1.066 2.133 120 545 1.357 .71 120 2090 9190 101 113 119 131 0 301 84 217 1.52 284 200 .658 1.351 .604 .434
4 1542 502 47 62 1495 440 1658 513 52 66 1611 451 0 0 419 167 69 27 100 100 100 100 1935 2062 3.398 .294 .28 .284 .311 1.855 120 601 .26 .82 130 2280 9190 100 113 137 150 0 669 83 587 .392 684 601 2.548 .373 -1.35 -1.422
5 203 202 48 71 155 131 209 197 49 73 161 126 0 0 47 65 10 26 100 95 100 88 286 287 1.183 .845 .783 .781 .808 2.042 120 527 .914 .7 120 2460 9190 101 113 156 168 0 269 95 175 1.127 263 168 .887 1.043 .172 .061
6 314 182 48 73 266 109 318 178 50 76 270 105 0 0 85 62 10 28 100 90 99 78 375 375 2.44 .41 .389 .377 .398 2.001 120 609 .397 .74 130 2650 9190 100 113 174 187 0 243 97 145 .546 237 140 1.83 .519 -.872 -.948
7 145 184 51 86 94 98 147 184 53 91 96 98 0 0 27 66 13 37 100 81 99 60 192 194 .959 1.043 1.021 .912 1.048 2.409 120 536 1.587 .63 120 2830 9180 100 112 193 205 0 245 115 131 1.39 245 131 .719 1.361 .475 .445
8 915 365 50 75 865 290 986 364 52 83 936 289 0 0 317 145 13 42 98 95 97 89 1155 1225 2.983 .335 .309 .338 .319 2.855 156 629 .312 .82 140 3020 9190 100 114 211 225 0 487 100 387 .447 485 385 2.237 .412 -1.162 -1.28
9 350 774 47 61 303 713 387 825 50 64 340 764 0 0 110 316 13 26 96 99 95 98 1016 1104 .425 2.353 2.247 2.001 2.212 1.975 156 603 2.821 .84 140 3200 9190 100 114 229 243 0 1032 81 951 3.138 1100 1019 .319 2.996 1.65 1.583
10 187 334 48 63 139 271 192 332 51 71 144 269 0 0 44 116 14 33 100 99 100 97 410 413 .513 1.95 1.868 1.839 1.81 1.662 120 482 2.326 .84 120 3380 9190 101 113 248 260 0 445 84 361 2.6 443 359 .385 2.491 1.378 1.317
11 244 223 47 60 197 163 248 225 51 63 201 165 0 0 62 89 21 25 100 93 100 91 360 366 1.209 .827 .821 .781 .899 1.767 80 508 .967 .78 110 3550 9190 101 112 265 276 0 297 80 217 1.103 300 220 .906 1.095 .142 .13
12 155 134 47 65 108 69 155 133 51 69 108 68 0 0 31 46 15 25 100 82 100 61 177 176 1.565 .639 .63 .52 .585 2.301 80 494 .819 .59 110 3750 9200 102 113 285 296 0 179 87 92 .852 177 91 1.174 .84 -.231 -.252
13 207 142 49 70 158 72 212 140 51 75 163 70 0 0 53 56 12 32 100 73 100 50 230 233 2.194 .456 .429 .419 .466 2.234 120 572 .57 .69 120 3930 9180 100 112 303 315 0 189 93 96 .608 187 93 1.646 .573 -.719 -.804
14 355 238 47 69 308 169 378 249 49 73 331 180 0 0 80 74 14 32 100 96 100 88 477 511 1.822 .549 .544 .508 .543 1.826 120 652 .563 .79 130 4120 9180 99 112 321 334 0 317 92 225 .732 332 240 1.367 .725 -.451 -.464
15 1914 247 46 65 1868 182 1941 250 49 68 1895 185 0 0 405 73 17 27 100 96 100 95 2050 2080 10.264 .097 .098 .093 .096 1.561 120 622 .093 .86 130 4300 9180 99 112 339 352 0 329 87 243 .13 333 247 7.698 .13 -2.944 -2.942
16 312 1177 46 70 266 1107 316 1221 49 73 270 1151 0 0 60 288 14 30 100 100 100 100 1373 1421 .24 4.162 4.263 4.102 3.994 1.428 120 610 4.813 .88 130 4480 9180 99 112 357 370 0 1569 93 1476 5.549 1628 1535 .18 5.684 2.472 2.507
17 189 193 46 70 143 123 198 199 49 73 152 129 0 0 45 65 11 27 100 89 98 84 266 281 1.163 .86 .849 .841 .9 2.056 120 555 1.029 .76 120 4660 9180 100 112 376 388 0 257 93 164 1.147 265 172 .872 1.132 .198 .178
18 324 232 47 70 277 162 327 228 50 73 280 158 0 0 89 79 12 25 100 96 100 91 439 438 1.71 .585 .564 .557 .588 1.742 120 611 .603 .83 130 4840 9180 99 112 393 406 0 309 93 216 .78 304 211 1.282 .752 -.359 -.41
19 235 310 48 74 187 236 221 279 51 78 173 205 0 0 77 146 13 27 100 95 100 92 423 378 .792 1.262 1.185 1.185 1.237 1.732 80 500 1.457 .78 110 5020 9170 99 110 412 423 0 413 99 315 1.683 372 273 .594 1.58 .751 .66
20 123 109 47 68 76 41 126 105 49 71 79 37 0 0 25 39 10 24 100 58 96 38 117 116 1.854 .539 .468 .549 .605 2.43 80 452 .918 .46 100 5220 9170 100 110 433 443 0 145 91 55 .719 140 49 1.39 .624 -.475 -.679

Total number of rows: 13824

Table truncated, full table size 2863 Kbytes.




Supplementary data files not provided
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