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Sample GSM90003 Query DataSets for GSM90003
Status Public on Dec 30, 2005
Title Fraction 60-62
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 60-62
Organism Saccharomyces cerevisiae
Characteristics Fraction 60-62
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41749.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
1 439 243 46 40 393 203 411 236 49 51 365 196 0 0 175 97 19 80 100 88 100 75 596 561 1.936 .517 .537 .515 .495 1.382 52 385 .512 .93 90 1220 19530 20 29 37 46 0 1104 182 922 2.346 1072 890 .426 2.439 1.23 1.286
2 9112 133 48 42 9064 91 9177 123 50 46 9129 81 0 0 4556 56 17 17 100 93 100 87 9155 9210 99.604 .01 .009 .016 .015 1.427 80 462 .009 .88 100 1400 19530 20 30 55 65 0 604 191 413 .046 559 368 21.93 .04 -4.455 -4.633
3 7858 20430 47 44 7811 20386 8277 19887 47 48 8230 19843 0 0 3423 12531 8 20 100 100 100 100 28197 28073 .383 2.61 2.411 2.181 2.343 2.166 80 452 3.018 .93 100 1580 19530 20 30 73 83 0 92793 200 92593 11.854 90326 90127 .084 10.951 3.567 3.453
4 2649 540 46 40 2603 500 2638 553 46 41 2592 513 0 0 497 161 6 12 100 100 100 100 3103 3105 5.206 .192 .198 .184 .192 1.36 52 361 .185 .93 90 1740 19530 20 29 89 98 0 2453 182 2271 .872 2512 2330 1.146 .899 -.197 -.154
5 1038 314 44 39 994 275 1146 355 44 40 1102 316 0 0 402 125 6 11 100 98 100 96 1269 1418 3.615 .277 .287 .257 .266 2.045 80 462 .269 .94 100 1920 19530 20 30 107 117 0 1426 177 1249 1.257 1612 1435 .796 1.302 .33 .381
6 6620 159 44 38 6576 121 7676 171 44 40 7632 133 0 0 2561 60 6 11 100 97 100 87 6697 7765 54.347 .018 .017 .02 .019 1.531 80 452 .018 .91 100 2100 19530 20 30 125 135 0 722 173 550 .084 777 604 11.966 .079 -3.581 -3.659
7 1031 571 42 37 989 534 1173 691 43 38 1131 654 0 0 369 250 5 10 100 98 100 96 1523 1785 1.852 .54 .578 .477 .524 1.724 80 452 .546 .94 100 2270 19520 19 29 142 152 0 2593 168 2425 2.452 3139 2970 .408 2.626 1.294 1.393
8 649 211 44 36 605 175 636 223 44 37 592 187 0 0 306 91 6 9 100 98 100 96 780 779 3.457 .289 .316 .278 .272 1.703 52 371 .268 .91 90 2440 19520 19 28 159 168 0 958 164 795 1.314 1013 849 .761 1.435 .394 .521
9 331 227 47 39 284 188 318 227 49 41 271 188 0 0 131 51 11 12 100 100 100 100 472 459 1.511 .662 .694 .684 .653 1.347 52 387 .58 .9 90 2610 19520 19 28 176 185 0 1031 177 854 3.007 1031 854 .333 3.151 1.588 1.656
10 364 239 48 39 316 200 320 222 50 41 272 183 0 0 212 143 11 11 100 96 100 86 516 455 1.58 .633 .673 .511 .639 2.383 52 328 .621 .89 80 2790 19520 20 28 195 203 0 1086 177 908 2.875 1008 831 .348 3.056 1.523 1.612
11 1395 123 45 38 1350 85 1491 132 46 40 1446 94 0 0 529 43 6 13 100 91 100 87 1435 1540 15.882 .063 .065 .062 .063 1.665 80 474 .057 .85 100 2970 19520 19 29 212 222 0 559 173 386 .286 600 427 3.497 .295 -1.806 -1.76
12 2000 167 46 39 1954 128 2151 180 47 40 2105 141 0 0 498 52 6 12 100 94 100 94 2082 2246 15.266 .066 .067 .065 .069 1.443 52 378 .066 .83 90 3140 19510 18 27 229 238 0 759 177 581 .298 818 640 3.361 .304 -1.749 -1.717
13 1455 95 46 39 1409 56 1557 92 47 41 1511 53 0 0 358 24 7 12 100 97 100 88 1465 1564 25.161 .04 .035 .037 .037 1.439 80 440 .037 .84 100 3320 19510 18 28 247 257 0 431 177 254 .181 418 241 5.54 .159 -2.47 -2.65
14 11779 5710 45 42 11734 5668 12130 6013 46 45 12085 5971 0 0 5217 3107 7 16 100 100 100 100 17402 18056 2.07 .483 .494 .4 .478 2.008 80 508 .496 .96 110 3480 19510 17 28 262 273 0 25935 191 25744 2.194 27311 27120 .456 2.244 1.134 1.166
15 1534 3753 44 39 1490 3714 1640 4276 45 40 1596 4237 0 0 448 1428 6 11 100 100 100 100 5204 5833 .401 2.493 2.655 2.335 2.565 1.533 80 536 2.702 .94 110 3660 19510 17 28 280 291 0 17046 177 16869 11.321 19422 19244 .088 12.058 3.501 3.592
16 1484 164 45 38 1439 126 1618 172 46 39 1573 134 0 0 355 40 7 10 100 100 100 100 1565 1707 11.421 .088 .085 .085 .087 1.346 52 386 .083 .92 90 3830 19510 18 27 298 307 0 745 173 572 .398 781 609 2.514 .387 -1.33 -1.37
17 642 111 45 37 597 74 617 113 46 39 572 76 0 0 162 22 6 11 100 100 100 98 671 648 8.068 .124 .133 .122 .122 1.44 52 388 .105 .83 90 4010 19510 18 27 316 325 0 504 168 336 .563 513 345 1.776 .603 -.829 -.729
18 2393 929 46 40 2347 889 2062 948 46 41 2016 908 0 0 1568 478 7 11 100 100 100 100 3236 2924 2.64 .379 .45 .43 .421 1.645 52 373 .338 .95 90 4180 19520 19 28 333 342 0 4220 182 4038 1.72 4306 4124 .581 2.046 .783 1.033
19 3397 166 47 41 3350 125 3757 170 48 42 3710 129 0 0 856 44 8 11 100 98 100 98 3475 3839 26.8 .037 .035 .037 .035 1.342 52 388 .038 .9 90 4350 19510 18 27 350 359 0 754 186 568 .169 772 586 5.901 .158 -2.561 -2.663
20 458 119 46 40 412 79 480 121 46 43 434 81 0 0 186 32 7 19 100 98 100 90 491 515 5.215 .192 .187 .2 .19 1.481 80 466 .173 .9 100 4530 19510 18 28 368 378 0 540 182 359 .871 550 368 1.148 .848 -.199 -.238

Total number of rows: 16128

Table truncated, full table size 3441 Kbytes.




Supplementary data files not provided
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