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Sample GSM89985 Query DataSets for GSM89985
Status Public on Dec 30, 2005
Title Fraction 84-86
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 84-86
Organism Saccharomyces cerevisiae
Characteristics Fraction 84-86
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41735.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
1 695 147 120 46 575 101 670 137 123 46 550 91 0 0 266 62 23 7 100 100 100 100 676 641 5.693 .176 .165 .159 .176 1.473 32 164 .185 .94 60 1280 18710 20 26 29 35 0 1033 323 710 1.234 963 639 .81 1.163 .304 .217
2 9926 3779 129 52 9797 3727 9082 2737 137 53 8953 2685 0 0 3887 2077 36 9 100 100 100 100 13524 11638 2.629 .38 .3 .364 .36 1.359 52 394 .395 .96 90 1450 18730 20 29 44 53 0 26552 365 26187 2.673 19231 18865 .374 2.107 1.418 1.075
3 24402 2311 170 57 24232 2254 26806 2674 166 57 26636 2617 0 0 8128 874 39 11 100 100 100 100 26486 29253 10.751 .093 .098 .091 .093 1.332 52 327 .092 .97 80 1640 18720 20 28 64 72 0 16238 400 15837 .654 18788 18388 1.53 .69 -.614 -.535
4 3429 984 181 58 3248 926 3826 1099 176 59 3645 1041 0 0 982 384 45 11 100 100 100 100 4174 4686 3.508 .285 .286 .25 .3 1.769 52 313 .291 .97 80 1800 18710 19 27 80 88 0 6914 408 6506 2.003 7722 7314 .499 2.007 1.002 1.005
5 1392 191 168 57 1224 134 1491 205 168 57 1323 148 0 0 279 44 47 12 100 98 100 96 1358 1471 9.134 .109 .112 .102 .115 1.476 52 326 .11 .95 80 1970 18710 19 27 97 105 0 1342 400 942 .769 1440 1040 1.3 .786 -.379 -.347
6 9146 1821 112 50 9034 1771 9541 1987 119 51 9429 1937 0 0 1218 445 37 10 100 100 100 100 10805 11366 5.101 .196 .205 .189 .207 1.294 52 326 .196 .97 80 2150 18710 19 27 115 123 0 12795 351 12443 1.377 13961 13610 .726 1.443 .462 .529
7 1536 194 86 44 1450 150 1607 206 88 44 1521 162 0 0 352 45 20 7 100 100 100 100 1600 1683 9.667 .103 .107 .102 .102 1.346 52 334 .101 .95 80 2320 18710 19 27 132 140 0 1363 309 1054 .727 1447 1138 1.376 .748 -.46 -.418
8 1014 235 88 43 926 192 874 202 90 43 786 159 0 0 593 139 21 7 100 98 100 96 1118 945 4.823 .207 .202 .182 .207 1.758 52 328 .213 .97 80 2510 18710 19 27 151 159 0 1651 302 1349 1.457 1419 1117 .686 1.421 .543 .507
9 496 181 102 44 394 137 502 184 105 44 400 140 0 0 77 34 28 9 100 100 100 100 531 540 2.876 .348 .35 .339 .347 1.29 52 328 .36 .95 80 2680 18710 19 27 168 176 0 1272 309 963 2.443 1293 984 .409 2.459 1.289 1.298
10 799 185 139 49 660 136 790 189 141 50 651 140 0 0 269 71 41 11 96 100 96 96 796 791 4.853 .206 .215 .205 .202 1.541 32 176 .21 .94 60 2860 18710 20 26 187 193 0 1300 344 956 1.448 1328 984 .691 1.511 .534 .596
11 1677 1296 110 42 1567 1254 1796 1470 114 44 1686 1428 0 0 346 439 39 10 100 100 100 100 2821 3114 1.25 .8 .847 .734 .833 1.535 52 328 .81 .94 80 3020 18700 18 26 202 210 0 9106 295 8811 5.623 10329 10033 .178 5.951 2.491 2.573
12 2143 597 93 38 2050 559 2324 625 92 39 2231 587 0 0 446 129 25 6 100 100 100 100 2609 2818 3.667 .273 .263 .273 .278 1.226 52 332 .267 .97 80 3200 18700 18 26 220 228 0 4195 267 3928 1.916 4391 4124 .522 1.849 .938 .886
13 1562 408 84 38 1478 370 1602 420 83 38 1518 382 0 0 252 62 21 6 100 100 100 100 1848 1900 3.995 .25 .252 .251 .255 1.152 52 379 .242 .97 90 3380 18710 18 27 237 246 0 2867 267 2600 1.759 2951 2684 .569 1.768 .815 .822
14 18393 1767 75 37 18318 1730 19526 1802 76 37 19451 1765 0 0 3978 362 18 7 100 100 100 100 20048 21216 10.588 .094 .091 .095 .093 1.214 52 386 .091 .97 90 3540 18700 17 26 253 262 0 12415 260 12155 .664 12661 12401 1.507 .638 -.592 -.649
15 1934 266 69 37 1865 229 1953 274 73 37 1884 237 0 0 294 39 21 6 100 100 100 100 2094 2121 8.144 .123 .126 .123 .123 1.218 52 326 .118 .96 80 3720 18700 18 26 272 280 0 1869 260 1609 .863 1925 1665 1.159 .884 -.213 -.178
16 1414 356 77 37 1337 319 1469 359 81 38 1392 322 0 0 247 50 24 7 100 100 100 100 1656 1714 4.191 .239 .231 .241 .239 1.229 52 320 .227 .96 80 3890 18700 18 26 289 297 0 2501 260 2241 1.676 2522 2262 .597 1.625 .745 .701
17 688 229 88 40 600 189 711 239 97 41 623 199 0 0 142 62 29 7 100 100 100 100 789 822 3.175 .315 .319 .297 .311 1.355 52 384 .32 .96 90 4070 18690 16 25 306 315 0 1609 281 1328 2.213 1679 1398 .452 2.244 1.146 1.166
18 2376 215 83 38 2293 177 2180 225 89 39 2097 187 0 0 1268 92 24 7 100 96 98 96 2470 2284 12.955 .077 .089 .077 .073 1.506 52 306 .074 .97 80 4230 18690 17 25 323 331 0 1511 267 1244 .542 1581 1314 1.844 .627 -.883 -.674
19 3691 599 86 43 3605 556 3820 614 102 43 3734 571 0 0 585 95 37 8 100 100 100 100 4161 4305 6.484 .154 .153 .154 .155 1.183 52 409 .15 .97 90 4420 18700 17 26 341 350 0 4209 302 3907 1.084 4314 4012 .923 1.074 .116 .104
20 810 127 122 45 688 82 801 126 132 45 679 81 0 0 132 17 50 10 100 100 100 100 770 760 8.39 .119 .119 .119 .124 1.249 32 230 .12 .94 70 4580 18690 17 24 358 365 0 892 316 576 .837 885 569 1.194 .838 -.256 -.255

Total number of rows: 16128

Table truncated, full table size 3474 Kbytes.




Supplementary data files not provided
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