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Sample GSM90638 Query DataSets for GSM90638
Status Public on Jan 05, 2006
Title skin cell line
Sample type RNA
 
Channel 1
Source name stratagene mouse reference
Organism Mus musculus
Characteristics stratagene mouse reference
Extracted molecule total RNA
Label Cy3
 
Channel 2
Source name skin cell line
Organism Mus musculus
Characteristics skin cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-10/21095.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 Jan 04, 2006
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 GPL3304
Series (2)
GSE3974 Contribution of unique genes by individual cell lines to Universal Mouse Reference RNA
GSE4389 Universal Reference RNA as a standard for microarray experiments

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 LOG_RAT2N_MEDIANs 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 LOG_RAT2N_MEDIAN of mean Channel 2 (usually 635 nm) intensity (CH2I_MEAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel
CH2BN_MEDIAN Normalized LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) background (CH2B_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale; Channel: Cy5 channel; Background
CH2DN_MEAN Normalized LOG_RAT2N_MEDIAN 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 LOG_RAT2N_MEDIAN of median Channel 2 (usually 635 nm) intensity (CH2I_MEDIAN/Normalization factor).; Type: integer; Scale: linear_scale
CH2DN_MEDIAN Normalized LOG_RAT2N_MEDIAN 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 6231 9054 148 218 6083 8836 7367 10459 158 236 7219 10241 0 0 4467 6073 66 134 85 87 82 84 14919 17460 .688 1.453 1.419 1.695 1.468 1.852 208 1068 1.419 .99 160 2970 4300 90 106 105 121 0 6514 157 6357 1.045 7524 7368 .957 1.021 .064 .029
2 516 563 144 210 372 353 562 551 158 227 418 341 0 0 186 266 76 109 88 83 84 67 725 759 1.054 .949 .816 .86 .905 2.065 156 700 1.18 .77 150 3170 4290 89 104 125 140 0 405 151 254 .683 396 245 1.465 .587 -.551 -.769
3 358 414 139 200 219 214 378 311 148 216 239 111 0 0 171 344 52 101 76 51 68 29 433 350 1.023 .977 .464 .808 .695 3.415 208 686 2.398 .5 160 3360 4300 90 106 144 160 0 298 144 154 .703 224 80 1.422 .334 -.508 -1.582
4 1635 1217 139 195 1496 1022 1558 1242 147 221 1419 1047 0 0 1226 763 47 126 81 79 77 75 2518 2466 1.464 .683 .738 .822 .684 2.139 208 676 .634 .94 160 3550 4290 89 105 163 179 0 876 140 735 .491 894 753 2.035 .531 -1.025 -.914
5 778 1119 146 208 632 911 882 1201 152 229 736 993 0 0 446 641 44 115 80 80 75 75 1543 1729 .694 1.441 1.349 1.543 1.375 1.987 208 737 1.506 .89 160 3740 4290 89 105 182 198 0 805 150 655 1.037 864 714 .964 .971 .052 -.043
6 583 538 145 211 438 327 641 282 151 228 496 71 0 0 298 653 45 105 81 42 77 29 765 567 1.339 .747 .143 .466 .329 4.95 208 717 2.828 .36 160 3930 4300 90 106 201 217 0 387 152 235 .537 203 51 1.862 .103 -.897 -3.28
7 5943 9179 144 212 5799 8967 5274 8017 153 228 5130 7805 0 0 3155 4818 49 103 98 100 97 98 14766 12935 .647 1.546 1.521 1.634 1.555 1.415 156 647 1.551 .99 150 4120 4290 89 104 220 235 0 6604 153 6451 1.112 5768 5615 .899 1.095 .154 .13
8 3226 6510 148 218 3078 6292 3139 6048 156 232 2991 5830 0 0 1578 3123 50 96 96 96 95 94 9370 8821 .489 2.044 1.949 2.076 2.026 1.319 156 669 2.045 .98 150 4310 4290 89 104 239 254 0 4683 157 4527 1.471 4351 4194 .68 1.402 .556 .488
9 1160 1702 143 209 1017 1493 1110 1789 149 227 967 1580 0 0 796 1023 47 157 80 82 78 77 2510 2547 .681 1.468 1.634 1.617 1.333 2.201 208 720 1.455 .87 160 4500 4300 90 106 258 274 0 1224 150 1074 1.056 1287 1137 .947 1.175 .079 .233
10 427 728 135 197 292 531 424 396 144 230 289 199 0 0 112 742 50 206 93 47 92 25 823 488 .55 1.818 .689 .927 .78 3.464 156 592 5.599 .56 150 4690 4300 90 105 277 292 -100 524 142 382 1.308 285 143 .764 .495 .388 -1.013
11 490 546 127 192 363 354 520 450 134 208 393 258 0 0 150 357 41 128 94 77 92 50 717 651 1.025 .975 .656 .753 .74 2.286 156 687 1.64 .65 150 4880 4290 89 104 296 311 0 393 138 255 .702 324 186 1.425 .472 -.511 -1.082
12 319 521 126 183 193 338 320 366 132 193 194 183 0 0 160 464 37 77 74 60 67 53 531 377 .571 1.751 .943 1.585 1.608 3.198 120 512 3.236 .68 120 5070 4280 90 102 317 329 0 375 132 243 1.26 263 132 .794 .679 .333 -.559
13 3200 2237 137 186 3063 2051 2886 2067 145 200 2749 1881 0 0 1957 1172 44 85 96 98 95 95 5114 4630 1.493 .67 .684 .723 .656 1.551 156 663 .633 .97 150 5260 4290 89 104 334 349 0 1609 134 1476 .482 1487 1353 2.076 .492 -1.054 -1.022
14 580 693 146 195 434 498 608 423 152 210 462 228 0 0 221 632 43 85 92 81 91 58 932 690 .871 1.147 .494 .716 .585 4.223 156 629 3.214 .37 150 5430 4300 90 105 351 366 -100 499 140 358 .826 304 164 1.211 .355 -.277 -1.494
15 418 684 140 195 278 489 432 528 146 205 292 333 0 0 188 564 41 81 82 81 77 72 767 625 .569 1.759 1.14 1.466 1.275 2.803 208 836 3.21 .66 170 5630 4300 89 106 370 387 -100 492 140 352 1.265 380 240 .79 .82 .34 -.286
16 2156 3268 143 216 2013 3052 2038 2818 150 225 1895 2602 0 0 1816 2375 44 86 84 88 82 84 5065 4497 .66 1.516 1.373 1.812 1.473 2.16 208 733 1.42 .97 160 5820 4300 90 106 390 406 0 2351 155 2196 1.091 2027 1872 .917 .988 .125 -.018
17 487 639 142 203 345 436 486 575 147 213 344 372 0 0 165 328 43 83 93 91 91 81 781 716 .791 1.264 1.081 1.101 1.093 2.285 156 706 1.75 .7 150 6020 4290 89 104 410 425 0 460 146 314 .909 414 268 1.1 .778 -.137 -.362
18 400 1037 136 190 264 847 361 751 140 196 225 561 0 0 242 896 39 77 78 68 68 66 1111 786 .312 3.208 2.493 2.643 2.836 2.636 120 490 4.669 .71 130 6210 4300 91 104 430 443 -100 746 137 609 2.308 540 404 .433 1.794 1.207 .843
19 538 871 136 186 402 685 565 782 140 196 429 596 0 0 269 571 36 82 82 84 80 79 1087 1025 .587 1.704 1.389 1.638 1.345 2.238 208 690 2.394 .69 160 6400 4300 90 106 448 464 0 627 134 493 1.226 563 429 .816 .999 .294 -.001
20 327 493 132 188 195 305 309 438 138 197 177 250 0 0 150 348 35 83 83 66 72 59 500 427 .639 1.564 1.412 1.391 1.544 2.588 156 558 2.396 .75 140 6600 4290 90 104 469 483 -100 355 135 219 1.125 315 180 .889 1.016 .17 .023

Total number of rows: 7680

Table truncated, full table size 1756 Kbytes.




Supplementary data files not provided
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