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Sample GSM82105 Query DataSets for GSM82105
Status Public on Nov 05, 2005
Title wt T240 parallel
Sample type RNA
 
Channel 1
Source name CRE reference pool
Organism Homo sapiens
Characteristics CRE reference pool
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name experimental sample
Organism Homo sapiens
Characteristics experimental sample
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Pathogen, cell line
Image: http://smd.stanford.edu/MicroArray/gifs/2001-01/12843.gif
Data processing VALUE is Log (base 2) of the ratio of the mean of Channel 2 (usually 635 nm) to Channel 1 (usually 532 nm)
 
Submission date Nov 04, 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 GPL2948
Series (1)
GSE3567 Listeria infection of Caco-2 cells

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
VALUE 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
LOG_RAT2N_MEDIAN 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 VALUE LOG_RAT2N_MEDIAN
1 3174 3238 182 182 2992 3056 1896 1556 215 221 1714 1374 0 0 2271 2588 121 138 100 100 100 100 6048 3088 .979 1.021 .802 .9 .959 1.845 80 456 1.083 .92 110 2010 17530 87 98 103 114 0 5544 312 5232 1.749 2664 2352 .572 1.372 .806 .457
2 6483 4201 171 170 6312 4031 6863 4309 185 192 6692 4139 0 0 1478 815 91 143 100 100 100 100 10343 10831 1.566 .639 .618 .649 .647 1.281 80 347 .621 .94 110 2170 17510 85 96 119 130 0 7192 291 6901 1.093 7377 7086 .915 1.059 .129 .083
3 2819 4057 174 172 2645 3885 3009 4461 260 259 2835 4289 0 0 963 1587 289 268 100 99 99 98 6530 7124 .681 1.469 1.513 1.387 1.497 1.618 120 398 1.569 .94 120 2310 17510 85 97 133 145 0 6946 294 6651 2.515 7637 7343 .398 2.59 1.33 1.373
4 1849 536 164 168 1685 368 1681 536 279 264 1517 368 0 0 794 200 360 284 98 58 91 16 2053 1885 4.579 .218 .243 .207 .224 1.846 80 348 .222 .57 100 2450 17500 85 95 148 158 0 918 288 630 .374 918 630 2.674 .415 -1.419 -1.268
5 9594 5840 169 164 9425 5676 10523 6508 316 249 10354 6344 0 0 5522 3672 431 244 100 95 97 92 15101 16698 1.661 .602 .613 .496 .613 2.323 80 359 .614 .95 100 2610 17500 85 95 164 174 0 9998 281 9718 1.031 11142 10861 .97 1.049 .044 .069
6 4797 3547 164 147 4633 3400 5063 3930 258 206 4899 3783 0 0 1413 1471 339 202 100 92 97 90 8033 8682 1.363 .734 .772 .565 .753 2.55 80 417 .785 .92 110 2760 17500 84 95 178 189 0 6073 252 5821 1.256 6728 6477 .796 1.322 .329 .403
7 1865 1439 165 136 1700 1303 1930 1480 171 140 1765 1344 0 0 365 314 51 33 100 100 100 100 3003 3109 1.305 .766 .761 .756 .792 1.261 52 325 .765 .87 90 2910 17500 85 94 194 203 0 2464 233 2231 1.312 2534 2301 .762 1.304 .392 .383
8 2036 2445 168 141 1868 2304 1980 2417 172 142 1812 2276 0 0 273 600 47 29 100 100 100 100 4172 4088 .811 1.233 1.256 1.201 1.238 1.369 52 334 1.293 .91 90 3060 17490 84 93 209 218 0 4186 241 3945 2.112 4138 3897 .474 2.15 1.078 1.105
9 27079 13149 165 141 26914 13008 27812 13766 167 144 27647 13625 0 0 8089 4994 45 35 100 100 100 100 39922 41272 2.069 .483 .493 .431 .489 2.244 80 431 .485 .89 110 3230 17490 83 94 225 236 0 22512 241 22270 .827 23568 23327 1.209 .844 -.273 -.245
10 1691 419 162 142 1529 277 1730 437 164 144 1568 295 0 0 459 124 41 36 98 93 98 91 1806 1863 5.52 .181 .188 .174 .181 1.785 80 341 .18 .88 100 3370 17490 84 94 240 250 0 717 243 474 .31 748 505 3.224 .322 -1.689 -1.634
11 2362 347 179 160 2183 187 2589 357 187 164 2410 197 0 0 794 92 56 34 98 92 98 85 2370 2607 11.674 .086 .082 .083 .079 2.072 80 358 .075 .8 100 3520 17490 84 94 255 265 0 594 274 320 .147 611 337 6.819 .14 -2.769 -2.837
12 8226 17199 200 187 8026 17012 9428 19331 242 216 9228 19144 0 0 3614 6943 169 142 96 100 91 100 25038 28372 .472 2.12 2.075 2.509 2.131 2.515 80 321 2.218 .91 100 3680 17490 84 94 271 281 0 29446 320 29126 3.629 33096 32776 .276 3.552 1.86 1.829
13 6583 4816 222 210 6361 4606 7960 5690 258 232 7738 5480 0 0 3055 2661 185 128 95 89 94 89 10967 13218 1.381 .724 .708 .619 .696 2.077 120 364 .749 .95 120 3820 17480 82 94 284 296 0 8245 360 7886 1.24 9742 9382 .807 1.212 .31 .278
14 27540 28237 205 194 27335 28043 22932 21518 402 208 22727 21324 0 2 12528 18186 2495 79 100 100 100 100 55378 44051 .975 1.026 .938 .849 .984 1.952 208 815 1.165 .95 160 3970 17500 82 98 297 313 0 48343 332 48011 1.756 36840 36508 .569 1.606 .813 .684
15 3943 2756 186 184 3757 2572 3951 2834 196 200 3765 2650 0 0 581 608 52 63 100 100 100 100 6329 6415 1.461 .685 .704 .664 .712 1.481 80 316 .683 .9 100 4130 17480 83 93 316 326 0 4718 315 4403 1.172 4852 4537 .853 1.205 .229 .269
16 8153 8244 182 171 7971 8073 8649 8489 192 176 8467 8318 0 0 2078 2315 54 40 100 100 100 100 16044 16785 .987 1.013 .982 .981 .983 1.483 80 344 1.038 .92 110 4280 17480 82 93 330 341 0 14114 293 13821 1.734 14534 14241 .577 1.682 .794 .75
17 17021 30683 172 140 16849 30543 20756 36947 179 144 20584 36807 0 0 6962 14030 51 42 100 100 100 100 47392 57391 .552 1.813 1.788 1.784 1.725 1.936 120 437 1.924 .94 120 4420 17470 81 93 344 356 0 52531 240 52291 3.104 63255 63016 .322 3.061 1.634 1.614
18 210 134 171 119 39 15 177 119 172 122 6 0 0 0 150 57 39 32 26 20 13 12 54 6 2.6 .385 null .831 .968 4.765 80 349 .244 .45 100 4570 17470 82 92 360 370 0 229 204 26 .658 204 0 1.519 null -.603 null
19 14909 16106 177 146 14732 15960 16518 16349 183 151 16341 16203 0 0 5655 5113 45 50 98 100 98 100 30692 32544 .923 1.083 .992 1.226 .971 2.097 80 357 1.054 .91 100 4730 17470 82 92 376 386 0 27574 250 27324 1.855 27990 27740 .539 1.698 .891 .763
20 6085 4704 188 178 5897 4526 6389 4847 195 184 6201 4669 0 0 1651 1596 52 53 100 100 100 100 10423 10870 1.303 .768 .753 .747 .752 1.49 80 356 .776 .92 100 4870 17470 82 92 390 400 0 8054 305 7749 1.314 8298 7994 .761 1.289 .394 .366

Total number of rows: 24192

Table truncated, full table size 5410 Kbytes.




Supplementary data files not provided
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