NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM90009 Query DataSets for GSM90009
Status Public on Dec 30, 2005
Title Fraction 44-46
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 44-46
Organism Saccharomyces cerevisiae
Characteristics Fraction 44-46
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Transcript size, RNA
Image: http://smd.stanford.edu/MicroArray/gifs/2003-06/41794.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
1 715 631 68 119 647 512 612 557 70 129 544 438 0 0 421 374 13 76 100 88 100 75 1159 982 1.264 .791 .805 .629 .748 2.319 52 392 .815 .91 90 1730 18110 18 27 32 41 0 2143 404 1739 2.688 1892 1488 .372 2.735 1.426 1.451
2 14264 347 75 119 14189 228 12830 307 79 122 12755 188 0 0 6214 154 17 38 100 92 100 82 14417 12943 62.232 .016 .015 .019 .017 1.662 52 326 .016 .82 80 1910 18100 18 26 51 59 0 1179 404 774 .055 1043 639 18.323 .05 -4.196 -4.32
3 21559 511 77 122 21482 389 23760 482 80 127 23683 360 0 0 10686 233 21 41 100 90 100 86 21871 24043 55.224 .018 .015 .021 .019 1.726 52 322 .017 .88 80 2080 18110 19 27 68 76 0 1736 414 1321 .062 1637 1223 16.259 .052 -4.023 -4.276
4 6152 387 79 123 6073 264 6513 398 84 131 6434 275 0 0 2616 122 24 44 100 96 100 94 6337 6709 23.004 .043 .043 .044 .043 1.64 52 326 .039 .86 80 2250 18100 18 26 85 93 0 1314 418 897 .148 1352 934 6.773 .145 -2.76 -2.784
5 2599 519 72 117 2527 402 2964 458 77 127 2892 341 0 0 1388 281 20 43 100 92 100 86 2929 3233 6.286 .159 .118 .149 .152 1.756 52 389 .146 .89 90 2430 18110 18 27 102 111 0 1763 397 1365 .54 1556 1158 1.851 .4 -.888 -1.32
6 15367 602 79 122 15288 480 16834 621 83 129 16755 499 0 0 4850 138 25 48 100 96 100 96 15768 17254 31.85 .031 .03 .032 .032 1.399 52 388 .029 .92 90 2600 18100 17 26 119 128 0 2045 414 1630 .107 2109 1695 9.378 .101 -3.229 -3.305
7 2931 583 85 120 2846 463 3248 596 91 124 3163 476 0 0 1013 157 25 41 100 100 100 98 3309 3639 6.147 .163 .15 .168 .169 1.455 52 396 .147 .93 90 2780 18100 17 26 137 146 0 1980 408 1573 .553 2024 1617 1.81 .511 -.856 -.968
8 1577 583 85 124 1492 459 1075 573 89 132 990 449 0 0 1135 288 22 44 100 96 100 94 1951 1439 3.251 .308 .454 .327 .312 2.377 52 322 .245 .83 80 2950 18100 18 26 155 163 0 1980 421 1559 1.045 1946 1525 .957 1.54 .063 .623
9 799 523 84 121 715 402 879 520 90 129 795 399 0 0 275 151 28 55 100 98 98 92 1117 1194 1.779 .562 .502 .573 .557 1.702 52 328 .548 .88 80 3120 18100 18 26 172 180 0 1776 411 1365 1.91 1766 1355 .524 1.705 .933 .769
10 973 581 83 120 890 461 757 605 86 124 674 485 0 0 636 267 21 36 100 100 96 96 1351 1159 1.931 .518 .72 .576 .586 1.905 32 176 .448 .89 60 3290 18100 19 25 190 196 0 1973 408 1566 1.759 2055 1647 .568 2.444 .815 1.289
11 4070 473 86 122 3984 351 4378 491 93 125 4292 369 0 0 1760 135 30 38 100 94 100 92 4335 4661 11.35 .088 .086 .094 .085 1.885 52 328 .075 .88 80 3470 18100 18 26 207 215 0 1607 414 1192 .299 1668 1253 3.342 .292 -1.741 -1.776
12 4497 524 85 119 4412 405 5009 574 93 123 4924 455 0 0 1415 179 31 33 100 100 100 98 4817 5379 10.894 .092 .092 .084 .095 1.534 52 322 .092 .94 80 3640 18100 18 26 224 232 0 1780 404 1376 .312 1950 1545 3.207 .314 -1.681 -1.672
13 3608 439 75 116 3533 323 4034 421 81 122 3959 305 0 0 1225 140 24 37 100 100 100 94 3856 4264 10.938 .091 .077 .092 .093 1.613 52 362 .082 .91 90 3810 18100 17 26 240 249 0 1491 394 1097 .311 1430 1036 3.22 .262 -1.687 -1.934
14 18159 686 71 119 18088 567 19223 676 75 124 19152 557 0 0 8719 265 20 57 100 96 100 92 18655 19709 31.901 .031 .029 .033 .032 1.771 52 387 .028 .81 90 3970 18090 16 25 256 265 0 2330 404 1926 .106 2296 1892 9.393 .099 -3.232 -3.34
15 4516 469 71 115 4445 354 4832 476 77 121 4761 361 0 0 1340 129 41 39 100 100 100 100 4799 5122 12.556 .08 .076 .079 .081 1.53 52 408 .078 .83 90 4150 18090 16 25 274 283 0 1593 391 1202 .27 1617 1226 3.697 .258 -1.886 -1.957
16 2777 433 68 116 2709 317 3098 437 70 124 3030 321 0 0 795 146 16 42 100 98 100 98 3026 3351 8.546 .117 .106 .115 .109 1.515 52 395 .108 .71 90 4330 18090 16 25 292 301 0 1471 394 1077 .397 1484 1090 2.516 .36 -1.331 -1.475
17 1419 375 68 120 1351 255 1580 388 71 123 1512 268 0 0 491 119 16 40 100 100 100 90 1606 1780 5.298 .189 .177 .189 .195 1.757 52 324 .164 .86 80 4500 18100 18 26 310 318 0 1274 408 866 .641 1318 910 1.56 .602 -.641 -.732
18 4386 654 78 120 4308 534 3371 712 85 129 3293 592 0 0 3244 279 32 50 100 94 100 90 4842 3885 8.067 .124 .18 .139 .151 1.92 52 330 .095 .87 80 4670 18100 18 26 327 335 0 2221 408 1814 .421 2418 2011 2.375 .611 -1.248 -.712
19 7119 514 86 121 7033 393 7757 511 91 138 7671 390 0 0 2375 134 25 144 100 94 100 86 7426 8061 17.896 .056 .051 .057 .055 1.571 52 320 .047 .63 80 4850 18090 17 25 345 353 0 1746 411 1335 .19 1736 1325 5.269 .173 -2.398 -2.534
20 1017 447 73 121 944 326 983 471 77 126 910 350 0 0 425 106 20 38 100 100 100 100 1270 1260 2.896 .345 .385 .372 .357 1.644 52 395 .306 .83 90 5020 18090 16 25 361 370 0 1518 411 1107 1.173 1600 1189 .853 1.306 .23 .386

Total number of rows: 16128

Table truncated, full table size 3580 Kbytes.




Supplementary data files not provided
| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap