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Sample GSM90628 Query DataSets for GSM90628
Status Public on Jan 05, 2006
Title Mammary tumor cell line
Sample type RNA
 
Channel 1
Source name stratagene mouse reference MRR
Organism Mus musculus
Characteristics stratagene mouse reference MRR
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/2001-08/19654.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 23182 8165 232 409 22950 7756 27483 9666 263 453 27251 9257 0 0 17182 5733 152 275 85 80 77 76 30706 36508 2.959 .338 .34 .427 .344 1.972 208 1045 .333 .99 170 2700 4080 47 64 53 70 0 6326 317 6009 .262 7489 7172 3.819 .263 -1.933 -1.926
2 716 877 237 409 479 468 818 880 268 456 581 471 0 0 385 501 150 292 68 61 66 41 947 1052 1.024 .977 .811 1.094 1.031 2.72 208 701 1.518 .72 160 2880 4080 48 64 72 88 0 679 317 363 .757 682 365 1.321 .628 -.402 -.671
3 484 655 203 388 281 267 482 586 242 429 279 198 0 0 221 351 170 241 72 43 28 21 548 477 1.052 .95 .71 .876 .917 2.671 156 574 2.147 .53 150 3080 4090 49 64 92 107 0 507 301 207 .736 454 153 1.358 .55 -.442 -.863
4 3607 2692 189 372 3418 2320 3735 2574 221 418 3546 2202 0 0 2961 2059 151 256 72 75 70 72 5738 5748 1.473 .679 .621 .864 .689 2.665 208 777 .683 .96 170 3260 4080 47 64 109 126 0 2086 288 1797 .526 1994 1706 1.902 .481 -.927 -1.056
5 775 937 180 358 595 579 834 929 202 404 654 571 0 0 479 500 109 223 75 70 71 56 1174 1225 1.028 .973 .873 1.019 1.012 2.51 208 771 1.097 .76 170 3450 4080 47 64 128 145 0 726 277 449 .754 720 442 1.326 .676 -.407 -.564
6 725 693 175 353 550 340 785 602 199 402 610 249 0 0 420 495 117 250 74 49 71 20 890 859 1.618 .618 .408 .7 .582 3.572 208 706 1.164 .57 170 3630 4090 48 65 146 163 0 537 273 263 .479 466 193 2.088 .316 -1.062 -1.661
7 18045 22717 196 389 17849 22328 18708 23333 223 443 18512 22944 0 0 14254 17801 122 289 82 84 78 79 40177 41456 .799 1.251 1.239 1.448 1.259 2.011 208 666 1.252 .99 160 3820 4080 48 64 166 182 0 17600 301 17299 .969 18078 17776 1.032 .96 -.045 -.059
8 6299 20477 230 487 6069 19990 7298 21344 249 544 7068 20857 0 0 4882 16323 115 356 79 82 75 75 26059 27925 .304 3.294 2.951 3.163 3.202 1.763 208 654 3.357 .99 160 4020 4080 48 64 186 202 0 15865 377 15488 2.552 16537 16159 .392 2.286 1.352 1.193
9 3023 3150 237 511 2786 2639 3147 3081 254 566 2910 2570 0 0 2178 2136 113 331 82 76 77 74 5425 5480 1.056 .947 .883 1.11 .982 1.888 208 697 .972 .96 170 4210 4080 47 64 204 221 0 2441 396 2045 .734 2387 1991 1.363 .684 -.446 -.547
10 446 632 207 427 239 205 472 612 231 491 265 185 0 0 205 313 124 354 67 31 52 5 444 450 1.166 .858 .698 1.177 1.205 3.077 208 648 2.756 .6 160 4390 4080 48 64 223 239 0 490 331 159 .665 474 143 1.505 .541 -.59 -.887
11 723 1072 176 370 547 702 765 1093 199 419 589 723 0 0 479 657 115 312 67 62 64 52 1249 1312 .779 1.283 1.228 1.604 1.435 2.695 208 718 1.613 .81 160 4590 4080 48 64 243 259 0 831 287 544 .994 847 560 1.006 .951 -.008 -.072
12 461 791 179 352 282 439 452 725 199 396 273 373 0 0 287 468 110 207 64 62 52 47 721 646 .642 1.557 1.366 1.628 1.755 3.049 120 469 2.218 .67 130 4780 4090 50 63 263 276 0 613 273 340 1.206 562 289 .829 1.059 .27 .082
13 3856 5466 191 388 3665 5078 4121 5804 214 430 3930 5416 0 0 3119 4210 104 237 77 79 73 72 8743 9346 .722 1.386 1.378 1.614 1.42 1.867 208 703 1.376 .98 160 4960 4090 49 65 280 296 0 4235 301 3934 1.073 4497 4196 .932 1.068 .102 .095
14 508 626 191 391 317 235 558 582 218 434 367 191 0 0 245 335 149 271 69 39 57 16 552 558 1.349 .741 .52 .9 .863 3.151 208 684 3.408 .56 160 5160 4090 49 65 300 316 0 485 303 182 .574 451 148 1.741 .403 -.8 -1.31
15 650 1121 187 379 463 742 631 1091 212 425 444 712 0 0 411 729 178 399 68 63 57 48 1205 1156 .624 1.603 1.604 1.675 1.641 2.343 208 766 1.901 .79 170 5340 4090 48 65 317 334 0 869 294 575 1.242 845 552 .805 1.242 .312 .313
16 8989 10347 204 407 8785 9940 8844 10753 225 436 8640 10346 0 0 7185 7694 137 228 83 84 79 81 18725 18986 .884 1.131 1.197 1.28 1.163 1.82 208 736 1.103 .99 170 5540 4090 48 65 337 354 0 8016 315 7701 .877 8331 8016 1.141 .928 -.19 -.108
17 625 835 201 375 424 460 658 813 220 409 457 438 0 0 354 440 96 212 72 65 65 50 884 895 .922 1.085 .958 1.294 1.199 2.769 208 700 1.38 .76 160 5730 4090 49 65 357 373 0 647 291 356 .841 630 339 1.19 .743 -.251 -.429
18 426 592 176 332 250 260 358 510 193 367 182 178 0 0 279 380 82 199 59 48 50 31 510 360 .962 1.04 .978 1.741 1.303 3.216 120 491 1.752 .69 130 5910 4090 50 63 376 389 0 459 257 201 .806 395 138 1.241 .758 -.312 -.4
19 550 953 166 318 384 635 604 996 182 348 438 678 0 0 319 539 82 180 71 74 66 65 1019 1116 .605 1.654 1.548 1.822 1.741 2.128 208 842 1.931 .8 170 6110 4090 48 65 394 411 0 738 246 492 1.281 772 525 .781 1.199 .357 .262
20 357 920 162 327 195 593 334 685 182 379 172 358 0 0 152 802 133 475 63 41 24 16 788 530 .329 3.041 2.081 2.2 2.464 3.541 120 443 5.934 .64 120 6310 4080 50 62 417 429 0 713 253 459 2.356 531 277 .424 1.613 1.236 .689

Total number of rows: 7680

Table truncated, full table size 1765 Kbytes.




Supplementary data files not provided
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