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Sample GSM89996 Query DataSets for GSM89996
Status Public on Dec 30, 2005
Title Fraction 66-68
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 66-68
Organism Saccharomyces cerevisiae
Characteristics Fraction 66-68
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41746.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 2475 636 282 195 2193 441 2290 583 288 199 2008 388 0 0 926 183 74 47 100 100 100 100 2634 2396 4.973 .201 .193 .203 .196 1.588 32 230 .19 .92 70 950 19410 17 24 35 42 0 3151 966 2185 .996 2888 1922 1.004 .957 -.005 -.063
2 20478 297 278 186 20200 111 20141 276 290 189 19863 90 0 0 6351 98 77 39 100 73 100 53 20311 19953 181.982 .005 .005 .014 .014 1.262 52 389 .005 .38 90 1120 19390 14 23 51 60 0 1471 921 550 .027 1367 446 36.733 .022 -5.199 -5.477
3 20628 8517 242 179 20386 8338 21066 7579 253 196 20824 7400 0 0 6255 3557 73 112 100 100 100 100 28724 28224 2.445 .409 .355 .381 .395 1.301 52 370 .437 .94 90 1300 19400 15 24 69 78 0 42195 887 41308 2.026 37548 36661 .494 1.761 1.019 .816
4 3448 335 159 179 3289 156 3245 328 170 192 3086 149 0 0 1155 79 52 88 100 76 100 40 3445 3235 21.083 .047 .048 .047 .049 1.533 52 361 .046 .82 90 1460 19410 16 25 85 94 0 1660 887 773 .235 1625 738 4.256 .239 -2.089 -2.064
5 1246 1676 114 183 1132 1493 1289 1653 118 192 1175 1470 0 0 211 269 33 66 100 100 100 100 2625 2645 .758 1.319 1.251 1.324 1.315 1.296 52 385 1.308 .94 90 1640 19410 16 25 103 112 0 8303 907 7397 6.534 8189 7283 .153 6.198 2.708 2.632
6 7605 280 83 138 7522 142 7865 302 87 140 7782 164 0 0 1447 68 24 62 100 80 100 67 7664 7946 52.972 .019 .021 .02 .021 1.31 52 395 .019 .7 90 1810 19400 15 24 120 129 0 1387 684 704 .094 1496 812 10.692 .104 -3.418 -3.26
7 1143 361 69 67 1074 294 1157 391 72 72 1088 324 0 0 202 85 18 29 100 100 100 100 1368 1412 3.653 .274 .298 .264 .271 1.312 52 388 .261 .91 90 1990 19410 16 25 138 147 0 1788 332 1457 1.356 1937 1605 .737 1.475 .44 .561
8 1683 339 65 53 1618 286 1482 331 66 57 1417 278 0 0 1248 191 11 34 100 94 100 80 1904 1695 5.657 .177 .196 .193 .168 2.127 52 321 .153 .91 80 2160 19400 16 24 156 164 0 1679 263 1417 .876 1640 1377 1.142 .972 -.191 -.041
9 322 196 65 50 257 146 341 206 66 53 276 156 0 0 66 54 11 31 100 96 100 86 403 432 1.76 .568 .565 .529 .568 1.477 52 323 .581 .92 80 2340 19400 16 24 174 182 0 971 248 723 2.814 1021 773 .355 2.8 1.493 1.486
10 1045 229 63 48 982 181 1017 234 64 49 954 186 0 0 642 106 10 10 100 93 100 93 1163 1140 5.425 .184 .195 .181 .177 2.025 32 236 .166 .92 70 2500 19400 16 23 190 197 0 1135 238 897 .913 1159 921 1.095 .966 -.131 -.05
11 836 119 61 50 775 69 890 121 61 53 829 71 0 0 184 24 9 37 100 88 100 42 844 900 11.232 .089 .086 .085 .091 1.547 52 393 .08 .86 90 2690 19400 15 24 208 217 0 590 248 342 .441 599 352 2.267 .424 -1.181 -1.237
12 893 253 61 51 832 202 993 287 61 54 932 236 0 0 401 103 9 35 100 88 98 82 1034 1168 4.119 .243 .253 .24 .242 1.678 80 454 .235 .94 100 2870 19400 15 25 226 236 0 1253 253 1001 1.203 1422 1169 .831 1.255 .266 .327
13 876 165 62 52 814 113 953 169 63 60 891 117 0 0 227 46 11 87 100 70 100 11 927 1008 7.204 .139 .131 .133 .136 1.482 80 418 .133 .41 100 3040 19400 15 25 243 253 0 817 258 560 .688 837 580 1.454 .651 -.54 -.62
14 8912 6013 61 53 8851 5960 9881 6328 62 65 9820 6275 0 0 3693 3040 10 110 100 100 100 100 14811 16095 1.485 .673 .639 .666 .68 1.548 80 430 .696 .97 100 3200 19400 15 25 259 269 0 29790 263 29527 3.336 31350 31088 .3 3.166 1.738 1.663
15 853 492 60 55 793 437 922 534 61 62 862 479 0 0 258 173 8 72 100 95 100 90 1230 1341 1.815 .551 .556 .523 .558 1.412 80 456 .556 .95 100 3380 19400 15 25 277 287 0 2437 272 2165 2.73 2646 2373 .366 2.753 1.449 1.461
16 888 202 59 54 829 148 945 191 59 57 886 137 0 0 188 72 10 27 100 98 100 98 977 1023 5.601 .179 .155 .161 .165 1.563 52 365 .186 .89 90 3550 19390 14 23 294 303 0 1001 268 733 .884 946 679 1.131 .766 -.177 -.384
17 316 173 58 51 258 122 324 177 59 53 266 126 0 0 73 50 10 14 100 100 100 96 380 392 2.115 .473 .474 .444 .465 1.506 52 382 .462 .87 90 3720 19400 15 24 311 320 0 857 253 604 2.343 877 624 .427 2.347 1.228 1.231
18 1654 343 55 51 1599 292 1684 308 56 55 1629 257 0 0 775 202 8 32 100 90 100 87 1891 1886 5.476 .183 .158 .156 .17 1.935 120 683 .189 .9 130 3900 19370 10 23 327 340 0 1699 253 1447 .905 1526 1273 1.105 .782 -.144 -.355
19 1292 1683 54 56 1238 1627 1516 1826 55 61 1462 1770 0 0 529 777 8 36 100 100 100 100 2865 3232 .761 1.314 1.211 1.27 1.299 1.633 80 417 1.365 .95 100 4070 19400 15 25 346 356 0 8338 277 8061 6.511 9046 8769 .154 5.998 2.703 2.584
20 307 191 53 58 254 133 313 186 54 68 260 128 0 0 57 43 7 75 100 94 100 30 387 388 1.91 .524 .492 .507 .522 1.473 52 362 .962 .49 90 4230 19390 14 23 362 371 0 946 287 659 2.594 921 634 .385 2.439 1.375 1.286

Total number of rows: 16128

Table truncated, full table size 3429 Kbytes.




Supplementary data files not provided
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