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Sample GSM87492 Query DataSets for GSM87492
Status Public on Dec 15, 2005
Title delYPL230w_stationary_phase_9hours
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 (9 hours)
Organism Saccharomyces cerevisiae
Characteristics delYPL230w, stationary phase (9 hours)
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Mutants, YPD-stationary-phase
Image: http://smd.stanford.edu/MicroArray/gifs/2002-10/33781.gif
Measurement: time(absolute) 9 h
name: 33781_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 5767 1860 52 58 5715 1802 6283 1842 57 66 6231 1784 0 0 1537 856 19 54 100 96 100 94 7517 8015 3.171 .315 .286 .3 .304 1.848 156 767 .307 .86 140 1990 9460 119 133 84 98 0 2385 74 2310 .404 2362 2287 2.474 .367 -1.307 -1.446
2 1768 256 52 57 1716 199 1720 225 57 62 1668 168 0 0 600 131 21 29 100 96 100 91 1915 1836 8.623 .116 .101 .104 .111 1.858 156 567 .112 .8 140 2180 9460 119 133 103 117 0 328 73 255 .149 288 215 6.726 .129 -2.75 -2.953
3 372 227 51 55 321 172 374 218 57 61 323 163 0 0 91 90 22 36 100 92 100 84 493 486 1.866 .536 .505 .495 .529 1.97 156 562 .565 .76 140 2360 9460 119 133 121 135 0 291 71 221 .687 279 209 1.456 .647 -.542 -.628
4 4292 760 49 52 4243 708 4741 795 55 56 4692 743 0 0 1480 375 19 36 100 94 100 91 4951 5435 5.993 .167 .158 .156 .165 1.908 156 575 .16 .87 140 2540 9460 119 133 139 153 0 974 67 908 .214 1019 953 4.674 .203 -2.225 -2.3
5 328 198 51 57 277 141 346 190 56 61 295 133 0 0 99 91 20 27 100 91 98 79 418 428 1.965 .509 .451 .453 .525 2.168 156 583 .532 .77 140 2720 9460 119 133 157 171 0 254 73 181 .653 244 171 1.532 .578 -.616 -.791
6 1032 313 53 54 979 259 1128 326 58 60 1075 272 0 0 304 121 21 31 99 92 99 92 1238 1347 3.78 .265 .253 .261 .264 1.908 156 651 .244 .82 140 2900 9460 119 133 175 189 0 401 69 332 .339 418 349 2.948 .324 -1.56 -1.624
7 212 161 52 56 160 105 209 152 60 61 157 96 0 0 65 62 25 32 98 88 95 71 265 253 1.524 .656 .611 .605 .626 2.004 120 537 .7 .67 130 3090 9470 120 133 194 207 0 206 72 135 .841 195 123 1.189 .784 -.249 -.351
8 2905 787 52 54 2853 733 3212 817 61 57 3160 763 0 0 823 343 30 25 100 94 99 94 3586 3923 3.892 .257 .241 .246 .245 1.815 156 583 .247 .87 140 3270 9460 119 133 212 226 0 1009 69 940 .329 1047 978 3.036 .31 -1.602 -1.692
9 736 836 54 59 682 777 846 876 62 65 792 817 0 0 268 257 29 31 94 100 94 98 1459 1609 .878 1.139 1.032 1.206 1.063 2.284 156 530 1.129 .87 140 3450 9470 120 134 230 244 0 1072 76 996 1.461 1123 1047 .685 1.323 .547 .403
10 441 697 53 57 388 640 469 714 62 63 416 657 0 0 142 243 31 30 100 100 99 99 1028 1073 .606 1.649 1.579 1.658 1.556 1.801 120 511 1.825 .83 130 3620 9470 120 133 247 260 0 894 73 821 2.115 915 842 .473 2.025 1.08 1.018
11 594 533 55 61 539 472 602 544 64 66 547 483 0 0 187 192 34 30 100 99 100 99 1011 1030 1.142 .876 .883 .835 .891 1.775 120 615 .901 .88 130 3800 9460 119 132 265 278 0 683 78 605 1.123 697 619 .891 1.132 .167 .179
12 237 191 53 61 184 130 248 190 64 69 195 129 0 0 66 75 41 41 98 86 91 72 314 324 1.415 .707 .662 .644 .709 2.662 120 635 .802 .68 130 3990 9450 118 131 284 297 0 245 78 167 .906 244 165 1.104 .848 -.143 -.238
13 389 247 54 61 335 186 391 237 63 70 337 176 0 0 153 110 36 59 98 89 95 67 521 513 1.801 .555 .522 .55 .513 2.178 156 638 .59 .65 140 4170 9460 119 133 302 316 0 317 78 238 .712 304 226 1.405 .67 -.49 -.579
14 767 534 59 58 708 476 772 545 70 68 713 487 0 0 257 213 40 57 99 95 98 93 1184 1200 1.487 .672 .683 .623 .622 2.226 120 582 .668 .73 130 4350 9460 119 132 320 333 0 685 74 610 .862 699 624 1.16 .876 -.214 -.192
15 4992 564 59 57 4933 507 5405 589 68 62 5346 532 0 0 1672 195 34 30 100 99 100 97 5440 5878 9.73 .103 .1 .105 .1 1.929 156 677 .09 .86 140 4540 9460 119 133 339 353 0 723 73 650 .132 755 682 7.589 .128 -2.924 -2.971
16 1119 2439 55 60 1064 2379 1248 2483 64 65 1193 2423 0 0 355 991 29 31 99 99 98 98 3443 3616 .447 2.236 2.031 2.099 2.142 2.463 156 607 2.565 .87 140 4730 9460 119 133 358 372 0 3127 77 3050 2.867 3183 3106 .349 2.604 1.519 1.381
17 500 481 52 57 448 424 510 489 59 65 458 432 0 0 101 140 22 45 100 100 100 99 872 890 1.057 .946 .943 .915 .947 1.536 120 495 1.051 .85 130 4900 9460 119 132 375 388 0 617 73 544 1.213 627 554 .824 1.209 .279 .274
18 739 587 54 58 685 529 818 567 61 77 764 509 0 0 233 310 25 209 99 89 99 69 1214 1273 1.295 .772 .666 .73 .698 2.225 156 647 1.172 .57 140 5080 9460 119 133 393 407 0 753 74 678 .99 727 653 1.01 .854 -.014 -.227
19 263 212 54 59 209 153 264 209 62 76 210 150 0 0 54 70 26 210 99 15 99 0 362 360 1.366 .732 .714 .69 .652 1.782 120 629 .719 .74 130 5260 9460 119 132 411 424 0 272 76 196 .939 268 192 1.065 .916 -.092 -.127
20 199 149 52 58 147 91 197 146 61 73 145 88 0 0 63 59 26 167 95 10 94 0 238 233 1.615 .619 .607 .612 .668 2.535 120 630 .634 .61 130 5450 9460 119 132 430 443 0 191 74 117 .794 187 113 1.26 .778 -.333 -.362

Total number of rows: 13824

Table truncated, full table size 2872 Kbytes.




Supplementary data files not provided
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