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Sample GSM90630 Query DataSets for GSM90630
Status Public on Jan 05, 2006
Title Mammary tumor cell line #2
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 Mammary tumor cell line
Organism Mus musculus
Characteristics Mammary tumor cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/19889.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 3364 2082 301 428 3063 1654 2830 2175 306 444 2529 1747 0 0 2428 1225 64 152 91 85 84 79 4717 4276 1.852 .54 .691 .644 .531 2.182 156 809 .506 .94 140 3160 4180 39 53 65 79 0 1707 351 1356 .443 1783 1432 2.259 .566 -1.176 -.821
2 584 772 269 385 315 387 547 693 270 402 278 308 0 0 236 402 61 149 80 72 73 51 702 586 .814 1.229 1.108 1.228 1.188 2.614 156 601 1.743 .72 140 3360 4190 40 54 85 99 0 633 316 317 1.007 568 252 .993 .908 .01 -.139
3 573 748 274 414 299 334 516 660 278 432 242 246 0 0 237 367 67 168 83 60 72 40 633 488 .895 1.117 1.017 1.127 1.082 2.733 120 482 1.651 .71 120 3540 4180 40 52 104 116 0 613 339 274 .916 541 202 1.092 .833 -.127 -.263
4 2253 1451 261 401 1992 1050 1950 1234 335 442 1689 833 0 0 1857 945 1707 765 49 51 22 28 3042 2522 1.897 .527 .493 .613 .514 2.061 156 699 .455 .97 150 3730 4180 38 53 121 136 0 1189 329 861 .432 1011 683 2.315 .404 -1.211 -1.307
5 986 949 215 299 771 650 1125 826 283 346 910 527 0 0 664 673 1694 759 7 40 0 10 1421 1437 1.186 .843 .579 .957 .812 2.864 208 711 .478 .93 160 3930 4190 39 55 141 157 0 778 245 533 .691 677 432 1.447 .475 -.533 -1.075
6 564 458 178 233 386 225 636 413 187 250 458 180 0 0 312 298 60 111 68 58 66 41 611 638 1.716 .583 .393 .663 .557 2.743 208 668 .799 .7 160 4110 4180 38 54 159 175 0 375 191 184 .478 339 148 2.093 .322 -1.066 -1.634
7 6001 7156 193 270 5808 6886 5386 6315 246 341 5193 6045 0 0 5085 6113 174 277 87 85 83 79 12694 11238 .843 1.186 1.164 1.253 1.185 1.817 208 642 1.198 .98 160 4310 4180 38 54 179 195 0 5866 221 5644 .972 5176 4955 1.029 .954 -.041 -.068
8 3537 7911 202 290 3335 7621 3433 7123 270 425 3231 6833 0 0 2805 6371 199 418 84 84 77 79 10956 10064 .438 2.285 2.115 2.316 2.213 1.75 208 705 2.328 .97 170 4490 4180 37 54 196 213 0 6484 238 6247 1.873 5839 5601 .534 1.733 .905 .794
9 1433 1420 189 278 1244 1142 1311 1442 228 370 1122 1164 0 0 1114 946 141 372 75 69 70 65 2386 2286 1.089 .918 1.037 1.098 .973 1.996 208 646 .917 .92 160 4690 4180 38 54 217 233 0 1164 228 936 .752 1182 954 1.329 .85 -.41 -.234
10 448 479 190 271 258 208 488 465 199 286 298 194 0 0 192 200 63 122 75 61 69 39 466 492 1.24 .806 .651 .94 .85 2.953 208 708 1.051 .69 170 4880 4180 37 54 235 252 0 393 222 170 .661 381 159 1.513 .534 -.598 -.906
11 566 693 175 240 391 453 626 676 180 249 451 436 0 0 300 387 49 109 75 73 72 66 844 887 .863 1.159 .967 1.333 1.244 2.431 208 774 1.299 .87 170 5070 4180 37 54 254 271 0 568 197 371 .95 554 357 1.053 .792 -.075 -.336
12 795 1097 158 216 637 881 700 1042 169 229 542 826 0 0 540 778 52 101 85 75 75 66 1518 1368 .723 1.383 1.524 1.321 1.422 1.933 120 477 1.45 .95 130 5250 4190 40 53 274 287 0 899 177 722 1.134 854 677 .882 1.249 .181 .321
13 2776 3666 159 210 2617 3456 3019 3899 170 224 2860 3689 0 0 2217 2966 50 98 85 84 76 76 6073 6549 .757 1.321 1.29 1.427 1.352 1.95 208 720 1.338 .98 170 5450 4200 39 56 292 309 0 3005 172 2833 1.082 3196 3024 .924 1.057 .114 .08
14 623 441 154 197 469 244 732 450 162 208 578 253 0 0 340 233 61 98 75 66 71 56 713 831 1.922 .52 .438 .708 .592 3.051 208 749 .558 .77 170 5640 4180 37 54 311 328 0 361 161 200 .426 369 207 2.345 .359 -1.23 -1.479
15 452 511 150 191 302 320 526 515 158 205 376 324 0 0 226 279 61 96 72 71 69 62 622 700 .944 1.06 .862 1.086 1.172 2.248 208 713 1.204 .84 170 5830 4190 38 55 330 347 0 419 157 262 .869 422 266 1.151 .706 -.203 -.502
16 1832 3275 152 195 1680 3080 1715 2749 158 206 1563 2554 0 0 1486 2730 42 85 81 85 79 81 4760 4117 .545 1.833 1.634 1.894 1.791 1.778 208 791 1.879 .96 170 6020 4180 37 54 349 366 0 2684 160 2525 1.503 2253 2093 .665 1.339 .588 .422
17 460 615 157 201 303 414 520 629 161 216 363 428 0 0 239 326 44 90 74 76 69 70 717 791 .732 1.366 1.179 1.513 1.435 2.143 208 745 1.46 .85 160 6220 4190 39 55 370 386 0 504 165 339 1.12 516 351 .893 .966 .163 -.049
18 546 797 156 216 390 581 466 588 161 228 310 372 0 0 333 600 41 96 88 71 74 60 971 682 .671 1.49 1.2 1.247 1.476 2.111 120 465 1.742 .91 130 6400 4200 41 54 389 402 0 653 177 476 1.221 482 305 .819 .984 .288 -.024
19 422 533 152 201 270 332 490 538 158 212 338 337 0 0 209 296 44 91 74 71 71 62 602 675 .813 1.23 .997 1.399 1.406 2.119 208 696 1.438 .84 160 6590 4190 39 55 407 423 0 437 165 272 1.008 441 276 .992 .817 .011 -.291
20 546 1404 163 215 383 1189 537 949 167 230 374 734 0 0 340 1448 42 105 72 74 68 65 1572 1108 .322 3.104 1.963 2.372 2.342 2.512 208 626 4.572 .8 160 6780 4200 40 56 426 442 0 1151 176 975 2.545 778 602 .393 1.609 1.347 .686

Total number of rows: 7680

Table truncated, full table size 1754 Kbytes.




Supplementary data files not provided
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