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Sample GSM89991 Query DataSets for GSM89991
Status Public on Dec 30, 2005
Title Fraction 72-74
Sample type RNA
 
Channel 1
Source name Reference RNA
Organism Saccharomyces cerevisiae
Characteristics Reference RNA
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name Fraction 72-74
Organism Saccharomyces cerevisiae
Characteristics Fraction 72-74
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41729.gif
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 29, 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 GPL3292
Series (1)
GSE3932 Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae

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
1 714 448 94 75 620 373 662 435 97 78 568 360 0 0 277 144 27 25 100 100 100 100 993 928 1.662 .602 .634 .621 .649 1.263 32 170 .574 .96 60 1080 18450 14 20 37 43 0 1077 180 897 1.446 1046 865 .692 1.523 .532 .607
2 12264 610 124 85 12140 525 10952 535 127 89 10828 450 0 0 4654 319 42 25 100 100 100 100 12665 11278 23.124 .043 .042 .039 .043 1.43 52 396 .044 .94 90 1240 18460 13 22 51 60 0 1466 204 1262 .104 1286 1082 9.621 .1 -3.266 -3.324
3 18868 11945 123 85 18745 11860 18473 10097 129 92 18350 10012 0 0 5488 6006 48 36 100 100 100 100 30605 28362 1.581 .633 .546 .572 .627 1.406 52 392 .688 .95 90 1430 18450 12 21 70 79 0 28711 204 28506 1.521 24269 24064 .658 1.311 .605 .391
4 3558 463 97 83 3461 380 3777 496 99 85 3680 413 0 0 991 182 30 23 100 100 100 96 3841 4093 9.108 .11 .112 .096 .104 1.723 52 376 .112 .92 90 1600 18450 12 21 87 96 0 1113 199 913 .264 1192 993 3.789 .27 -1.922 -1.89
5 1344 1122 103 88 1241 1034 1346 1142 112 94 1243 1054 0 0 133 214 51 43 100 100 100 100 2275 2297 1.2 .833 .848 .813 .858 1.305 52 371 .853 .95 90 1760 18450 12 21 103 112 0 2697 212 2485 2.003 2745 2533 .499 2.038 1.002 1.027
6 3780 44345 117 86 3663 44259 4130 46320 124 99 4013 46234 0 0 829 6228 42 53 100 100 100 100 47922 50247 .083 12.083 11.521 12.389 11.523 1.213 52 334 12.035 .97 80 1930 18460 14 22 121 129 0 106586 207 106379 29.042 111333 111126 .034 27.692 4.86 4.791
7 1388 1410 112 70 1276 1340 1405 1465 117 75 1293 1395 0 0 109 284 42 34 100 100 100 100 2616 2688 .952 1.05 1.079 1.024 1.1 1.297 52 402 1.107 .95 90 2110 18450 12 21 138 147 0 3389 168 3221 2.524 3521 3353 .396 2.593 1.336 1.375
8 2206 1425 102 63 2104 1362 2498 1445 107 69 2396 1382 0 0 865 749 28 36 100 100 100 100 3466 3778 1.545 .647 .577 .612 .601 1.386 32 230 .68 .93 70 2280 18450 13 20 156 163 0 3425 151 3274 1.556 3473 3322 .643 1.386 .638 .471
9 407 518 121 76 286 442 414 528 136 90 293 452 0 0 63 96 56 67 100 100 100 100 728 745 .647 1.545 1.543 1.548 1.555 1.26 32 236 1.699 .92 70 2440 18460 14 21 172 179 0 1245 183 1062 3.715 1269 1086 .269 3.708 1.893 1.891
10 1518 791 132 74 1386 717 1625 825 133 75 1493 751 0 0 532 234 36 23 100 100 100 100 2103 2244 1.933 .517 .503 .537 .528 1.391 32 176 .486 .95 60 2620 18460 15 21 191 197 0 1901 178 1723 1.243 1983 1805 .804 1.209 .314 .274
11 1748 250 115 75 1633 175 1831 258 119 77 1716 183 0 0 333 59 37 21 100 100 100 100 1808 1899 9.331 .107 .107 .103 .103 1.495 52 402 .1 .89 90 2790 18450 12 21 206 215 0 601 180 421 .258 620 440 3.882 .256 -1.957 -1.964
12 2001 6782 108 70 1893 6712 1987 6926 109 72 1879 6856 0 0 208 947 28 20 100 100 100 100 8605 8735 .282 3.546 3.649 3.53 3.608 1.152 52 400 3.641 .98 90 2970 18450 12 21 224 233 0 16301 168 16133 8.522 16647 16479 .117 8.77 3.091 3.133
13 1432 1623 116 73 1316 1550 1419 1609 124 75 1303 1536 0 0 184 168 39 20 100 100 100 100 2866 2839 .849 1.178 1.179 1.181 1.173 1.13 52 379 1.164 .96 90 3150 18460 13 22 242 251 0 3901 175 3726 2.831 3867 3692 .353 2.833 1.501 1.503
14 10980 11560 110 71 10870 11489 11714 12609 122 76 11604 12538 0 0 3522 4803 44 27 100 100 100 100 22359 24142 .946 1.057 1.08 .976 1.096 1.456 80 454 1.104 .97 100 3320 18450 12 22 259 269 0 27785 171 27615 2.54 30307 30136 .394 2.597 1.345 1.377
15 1533 1482 122 74 1411 1408 1660 1658 128 76 1538 1584 0 0 446 476 47 23 100 100 100 100 2819 3122 1.002 .998 1.03 .955 .999 1.542 80 462 1.008 .96 100 3490 18450 12 22 276 286 0 3562 178 3384 2.398 3985 3807 .417 2.475 1.262 1.308
16 1357 1497 151 79 1206 1418 1353 1480 156 81 1202 1401 0 0 142 202 48 21 100 100 100 100 2624 2603 .85 1.176 1.166 1.173 1.18 1.151 52 384 1.146 .97 90 3660 18450 12 21 293 302 0 3598 190 3408 2.826 3557 3367 .354 2.801 1.499 1.486
17 688 295 179 84 509 211 688 295 174 85 509 211 0 0 83 39 48 21 100 100 100 100 720 720 2.412 .415 .415 .412 .418 1.279 52 326 .386 .91 80 3840 18450 13 21 312 320 0 709 202 507 .996 709 507 1.004 .996 -.005 -.005
18 3745 1643 175 91 3570 1552 3855 1770 176 96 3680 1679 0 0 957 413 48 25 100 100 100 100 5122 5359 2.3 .435 .456 .432 .422 1.219 32 230 .433 .98 70 4020 18450 13 20 330 337 0 3949 219 3730 1.045 4254 4036 .957 1.097 .063 .133
19 3285 3260 183 90 3102 3170 3318 3452 182 92 3135 3362 0 0 374 605 53 25 100 100 100 100 6272 6497 .979 1.022 1.072 1.007 1.05 1.188 52 401 1.053 .98 90 4200 18450 12 21 347 356 0 7836 216 7619 2.456 8297 8081 .407 2.578 1.296 1.366
20 705 353 207 103 498 250 698 359 227 109 491 256 0 0 138 47 90 34 100 100 100 100 748 747 1.992 .502 .521 .512 .502 1.309 32 236 .463 .91 70 4360 18460 14 21 364 371 0 848 248 601 1.207 863 615 .829 1.253 .271 .326

Total number of rows: 16128

Table truncated, full table size 3532 Kbytes.




Supplementary data files not provided
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