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Sample GSM90008 Query DataSets for GSM90008
Status Public on Dec 30, 2005
Title Fraction 46-48
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 46-48
Organism Saccharomyces cerevisiae
Characteristics Fraction 46-48
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41793.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
1 720 985 83 81 637 904 592 741 84 82 509 660 0 0 525 680 14 15 100 100 100 100 1541 1169 .705 1.419 1.297 1.481 1.458 1.41 52 314 1.384 .94 80 1400 18450 33 41 28 36 0 4570 376 4194 6.584 3438 3062 .152 6.016 2.719 2.589
2 13093 222 85 82 13008 140 11085 210 86 86 11000 128 0 0 6407 77 17 47 100 90 100 63 13148 11128 92.914 .011 .012 .014 .013 1.51 52 386 .01 .7 90 1580 18440 31 40 45 54 0 1030 380 650 .05 974 594 20.026 .054 -4.324 -4.211
3 22176 447 84 82 22092 365 20872 381 88 87 20788 299 0 0 11568 227 17 48 100 94 100 86 22457 21087 60.526 .017 .014 .018 .018 1.48 52 328 .016 .93 80 1750 18440 32 40 63 71 0 2074 380 1693 .077 1768 1387 13.045 .067 -3.705 -3.905
4 4059 299 86 82 3973 217 4415 319 90 83 4329 237 0 0 1392 103 17 14 100 100 100 98 4190 4566 18.309 .055 .055 .052 .057 1.779 52 328 .052 .42 80 1930 18440 32 40 81 89 0 1387 380 1007 .253 1480 1100 3.946 .254 -1.98 -1.977
5 1601 308 88 83 1513 225 1711 341 91 85 1623 258 0 0 641 110 17 17 100 100 100 98 1738 1881 6.724 .149 .159 .148 .147 1.626 52 321 .143 .92 80 2100 18440 32 40 98 106 0 1429 385 1044 .69 1582 1197 1.449 .738 -.535 -.439
6 10995 397 87 83 10908 314 12030 416 90 83 11943 333 0 0 3340 83 18 15 100 100 100 98 11222 12276 34.739 .029 .028 .03 .028 1.372 52 387 .026 .95 90 2280 18430 30 39 115 124 0 1842 385 1457 .134 1930 1545 7.487 .129 -2.904 -2.95
7 1783 682 79 81 1704 601 1898 707 81 83 1819 626 0 0 524 176 15 35 100 100 100 100 2305 2445 2.835 .353 .344 .355 .342 1.345 52 328 .33 .95 80 2450 18430 31 39 133 141 0 3164 376 2788 1.636 3280 2904 .611 1.597 .711 .675
8 1326 465 73 81 1253 384 778 352 74 82 705 271 0 0 956 302 12 16 100 96 100 94 1637 976 3.263 .306 .384 .268 .292 1.767 52 328 .303 .97 80 2630 18430 31 39 151 159 0 2157 376 1782 1.422 1633 1257 .703 1.783 .508 .835
9 512 274 70 82 442 192 595 284 71 85 525 202 0 0 189 82 12 17 97 98 97 97 634 727 2.302 .434 .385 .462 .416 2.148 80 487 .402 .9 100 2810 18430 30 40 168 178 0 1271 380 891 2.015 1318 937 .496 1.785 1.011 .836
10 1062 450 79 87 983 363 1196 496 80 87 1117 409 0 0 563 194 16 17 100 100 100 100 1346 1526 2.708 .369 .366 .391 .378 1.52 32 236 .348 .95 70 2980 18420 30 37 186 193 0 2088 404 1684 1.713 2301 1898 .584 1.699 .777 .765
11 1864 300 87 86 1777 214 1871 321 88 86 1784 235 0 0 608 84 16 17 100 100 100 98 1991 2019 8.304 .12 .132 .115 .122 1.578 52 405 .104 .88 90 3150 18420 29 38 202 211 0 1392 399 993 .559 1489 1090 1.79 .611 -.84 -.71
12 2762 334 83 84 2679 250 2807 355 85 86 2724 271 0 0 735 89 19 20 100 100 100 100 2929 2995 10.716 .093 .099 .089 .093 1.528 52 395 .089 .9 90 3330 18420 29 38 220 229 0 1550 390 1160 .433 1647 1257 2.31 .462 -1.208 -1.115
13 2095 293 85 84 2010 209 2157 296 86 88 2072 212 0 0 658 71 16 33 100 98 100 94 2219 2284 9.617 .104 .102 .105 .107 1.478 52 386 .092 .91 90 3510 18410 28 37 238 247 0 1359 390 970 .482 1373 984 2.073 .475 -1.052 -1.075
14 21024 535 90 85 20934 450 22220 558 93 89 22130 473 0 0 7017 109 18 34 100 100 100 100 21384 22603 46.52 .021 .021 .023 .021 1.542 52 387 .019 .95 90 3680 18410 28 37 255 264 0 2482 394 2088 .1 2589 2195 10.027 .099 -3.326 -3.334
15 2392 316 83 83 2309 233 2373 318 85 89 2290 235 0 0 771 80 17 51 100 100 100 90 2542 2525 9.91 .101 .103 .101 .102 1.416 52 395 .095 .93 90 3850 18410 28 37 272 281 0 1466 385 1081 .468 1475 1090 2.136 .476 -1.095 -1.071
16 1881 330 76 84 1805 246 2060 338 78 91 1984 254 0 0 628 100 14 52 100 94 100 92 2051 2238 7.337 .136 .128 .134 .138 1.745 52 387 .125 .8 90 4030 18410 28 37 290 299 0 1531 390 1141 .632 1568 1178 1.581 .594 -.661 -.751
17 794 310 81 85 713 225 819 315 82 87 738 230 0 0 232 55 17 18 100 100 100 100 938 968 3.169 .316 .312 .328 .317 1.483 52 388 .267 .9 90 4200 18410 28 37 307 316 0 1438 394 1044 1.464 1461 1067 .683 1.446 .55 .532
18 2572 427 78 84 2494 343 2048 400 79 85 1970 316 0 0 2124 220 15 16 100 98 100 96 2837 2286 7.271 .138 .16 .158 .13 2.08 52 328 .111 .91 80 4380 18410 29 37 326 334 0 1981 390 1591 .638 1856 1466 1.567 .744 -.648 -.426
19 5277 355 80 85 5197 270 5705 380 81 87 5625 295 0 0 1712 83 16 19 100 100 100 98 5467 5920 19.248 .052 .052 .052 .052 1.395 52 322 .049 .95 80 4550 18410 29 37 343 351 0 1647 394 1253 .241 1763 1369 4.149 .243 -2.053 -2.039
20 739 341 84 85 655 256 743 353 85 88 659 268 0 0 264 68 15 25 100 100 100 100 911 927 2.559 .391 .407 .414 .431 1.666 52 396 .342 .88 90 4720 18400 27 36 359 368 0 1582 394 1188 1.813 1638 1243 .551 1.887 .859 .916

Total number of rows: 16128

Table truncated, full table size 3505 Kbytes.




Supplementary data files not provided
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