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Sample GSM89990 Query DataSets for GSM89990
Status Public on Dec 30, 2005
Title Fraction 88-90
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 88-90
Organism Saccharomyces cerevisiae
Characteristics Fraction 88-90
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41737.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 1757 393 260 96 1497 297 1863 408 278 98 1603 312 0 0 404 94 93 17 100 100 100 100 1794 1915 5.04 .198 .195 .195 .2 1.28 32 170 .197 .96 60 1520 18040 21 27 37 43 0 2764 675 2089 1.395 2869 2194 .717 1.369 .481 .453
2 18538 2262 275 98 18263 2164 17897 1869 308 102 17622 1771 0 0 6422 1222 125 25 100 100 100 100 20427 19393 8.439 .118 .1 .108 .115 1.472 52 322 .123 .94 80 1680 18040 20 28 52 60 0 15908 689 15219 .833 13144 12455 1.2 .707 -.263 -.501
3 32222 1892 244 90 31978 1802 34530 2031 265 92 34286 1941 0 0 8009 583 83 18 100 100 100 100 33780 36227 17.746 .056 .057 .055 .059 1.214 52 400 .056 .98 90 1870 18040 19 28 70 79 0 13306 633 12673 .396 14283 13650 2.523 .398 -1.335 -1.329
4 6845 1131 213 87 6632 1044 7548 1277 242 92 7335 1190 0 0 2162 428 125 26 100 100 100 100 7676 8525 6.352 .157 .162 .149 .157 1.287 52 384 .159 .98 90 2050 18040 19 28 88 97 0 7954 612 7342 1.107 8981 8369 .903 1.141 .147 .19
5 2750 277 212 92 2538 185 2848 282 246 98 2636 190 0 0 471 41 139 30 100 100 100 100 2723 2826 13.719 .073 .072 .072 .072 1.228 52 370 .071 .92 90 2210 18040 19 28 104 113 0 1948 647 1301 .513 1983 1336 1.951 .507 -.964 -.98
6 16999 2367 235 95 16764 2272 18120 2530 267 101 17885 2435 0 0 3249 524 109 31 100 100 100 100 19036 20320 7.379 .136 .136 .134 .137 1.135 52 371 .137 .99 90 2380 18040 19 28 121 130 0 16646 668 15978 .953 17793 17125 1.049 .957 -.069 -.063
7 2975 307 247 100 2728 207 3093 318 281 106 2846 218 0 0 562 52 147 32 100 100 100 98 2935 3064 13.179 .076 .077 .075 .076 1.254 52 314 .075 .96 80 2550 18030 19 27 139 147 0 2159 703 1456 .534 2236 1533 1.874 .539 -.906 -.892
8 3602 1155 267 108 3335 1047 4077 1211 293 116 3810 1103 0 0 1347 462 176 39 100 100 100 100 4382 4913 3.185 .314 .29 .304 .297 1.363 32 220 .307 .96 70 2730 18030 19 26 157 164 0 8123 760 7363 2.208 8517 7757 .453 2.036 1.143 1.026
9 883 386 249 108 634 278 901 396 346 651 652 288 0 0 174 65 401 3173 88 0 19 0 912 940 2.281 .438 .442 .447 .436 1.203 52 327 8.539 .79 80 2910 18040 20 28 175 183 0 2715 760 1955 3.084 2785 2025 .324 3.106 1.625 1.635
10 1983 621 249 102 1734 519 2007 589 276 112 1758 487 0 0 667 239 106 42 100 100 100 96 2253 2245 3.341 .299 .277 .285 .282 1.347 32 170 .299 .95 60 3080 18040 21 27 193 199 0 4367 717 3650 2.105 4142 3425 .475 1.948 1.074 .962
11 3680 986 233 86 3447 900 3814 1005 255 93 3581 919 0 0 592 173 106 36 100 100 100 100 4347 4500 3.83 .261 .257 .26 .266 1.138 52 332 .26 .98 80 3250 18040 20 28 209 217 0 6934 605 6329 1.836 7068 6463 .545 1.805 .877 .852
12 4380 675 142 66 4238 609 4597 717 159 68 4455 651 0 0 832 136 66 17 100 100 100 100 4847 5106 6.959 .144 .146 .142 .145 1.144 52 320 .143 .99 80 3430 18030 19 27 227 235 0 4747 464 4283 1.011 5042 4578 .99 1.028 .015 .039
13 3126 922 169 67 2957 855 2973 924 186 74 2804 857 0 0 878 227 95 65 100 100 100 100 3812 3661 3.458 .289 .306 .29 .284 1.277 52 371 .274 .96 90 3610 18040 19 28 244 253 0 6484 471 6013 2.033 6498 6027 .492 2.149 1.024 1.104
14 26832 1738 210 69 26622 1669 29505 1877 215 69 29295 1808 0 0 6774 533 64 11 100 100 100 100 28291 31103 15.951 .063 .062 .061 .06 1.26 52 372 .062 .97 90 3770 18030 18 27 260 269 0 12223 485 11738 .441 13200 12715 2.268 .434 -1.181 -1.204
15 3660 435 196 69 3464 366 3664 426 198 69 3468 357 0 0 597 81 38 10 100 100 100 100 3830 3825 9.464 .106 .103 .105 .105 1.137 52 389 .106 .98 90 3950 18040 19 28 278 287 0 3059 485 2574 .743 2996 2511 1.346 .724 -.428 -.466
16 2694 439 188 67 2506 372 2788 462 188 67 2600 395 0 0 439 64 51 12 100 100 100 100 2878 2995 6.737 .148 .152 .148 .146 1.127 52 387 .146 .99 90 4120 18030 18 27 295 304 0 3087 471 2616 1.044 3249 2778 .958 1.068 .062 .095
17 1426 1087 175 64 1251 1023 1433 1105 175 64 1258 1041 0 0 208 176 44 10 100 100 100 100 2274 2299 1.223 .818 .828 .816 .822 1.123 52 384 .807 .99 90 4310 18040 19 28 314 323 0 7645 450 7194 5.751 7771 7321 .174 5.82 2.524 2.541
18 4534 291 189 65 4345 226 4534 307 193 65 4345 242 0 0 2148 97 41 10 100 100 100 100 4571 4587 19.226 .052 .056 .054 .05 1.327 52 320 .049 .97 80 4480 18040 20 28 332 340 0 2047 457 1589 .366 2159 1702 2.734 .392 -1.451 -1.352
19 6808 521 191 66 6617 455 7108 537 194 66 6917 471 0 0 1273 104 41 10 100 100 100 100 7072 7388 14.543 .069 .068 .068 .07 1.182 52 384 .068 .98 90 4650 18040 19 28 348 357 0 3664 464 3200 .484 3777 3312 2.068 .479 -1.048 -1.062
20 1420 428 144 59 1276 369 1436 437 152 59 1292 378 0 0 294 99 38 9 100 100 100 100 1645 1670 3.458 .289 .293 .283 .286 1.188 52 386 .291 .98 90 4820 18040 19 28 365 374 0 3010 415 2595 2.034 3073 2658 .492 2.058 1.024 1.041

Total number of rows: 16128

Table truncated, full table size 3516 Kbytes.




Supplementary data files not provided
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