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Sample GSM90639 Query DataSets for GSM90639
Status Public on Jan 05, 2006
Title T-cell Lymphoma 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 T-cell Lymphoma cell line
Organism Mus musculus
Characteristics T-cell Lymphoma cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20141.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) [email protected]
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 12465 11372 150 415 12315 10957 14802 12120 160 522 14652 11705 0 0 5994 6018 73 519 92 91 91 89 23272 26357 1.124 .89 .799 .943 .837 1.718 156 901 .921 .91 150 2690 4180 62 77 61 76 0 12228 446 11782 .957 13032 12586 1.045 .859 -.064 -.219
2 501 728 134 400 367 328 547 732 153 516 413 332 0 0 187 342 80 649 87 12 82 1 695 745 1.119 .894 .804 .894 .897 3.182 156 615 3.982 .42 140 2880 4180 63 77 81 95 0 783 430 353 .961 787 357 1.041 .864 -.057 -.21
3 311 590 122 397 189 193 302 479 147 587 180 82 0 0 150 770 91 1279 74 1 48 1 382 262 .979 1.021 .456 1.116 1.188 3.582 156 670 18.417 .32 150 3060 4180 62 77 98 113 0 634 427 208 1.098 515 88 .911 .49 .135 -1.03
4 3665 5332 113 363 3552 4969 3910 5315 128 515 3797 4952 0 0 1676 2621 74 1026 91 89 91 85 8521 8749 .715 1.399 1.304 1.439 1.355 1.596 156 636 1.479 .94 150 3250 4180 62 77 117 132 0 5733 390 5343 1.504 5715 5325 .665 1.402 .589 .488
5 335 828 98 331 237 497 284 661 116 510 186 330 0 0 237 1195 74 1258 60 6 54 2 734 516 .477 2.097 1.774 2.23 1.768 3.367 256 981 26.035 .28 180 3450 4190 62 80 136 154 0 890 356 534 2.255 711 355 .443 1.908 1.173 .932
6 449 1832 95 337 354 1495 444 1608 110 510 349 1271 0 0 194 1080 63 1284 90 48 86 12 1849 1620 .237 4.223 3.642 3.987 3.883 1.945 156 628 14.071 .56 150 3630 4180 62 77 155 170 0 1970 362 1608 4.541 1729 1367 .22 3.916 2.183 1.969
7 9270 5585 95 320 9175 5265 10855 5811 107 408 10760 5491 0 0 7291 4362 50 400 84 78 79 74 14440 16251 1.743 .574 .51 .839 .557 3.038 208 760 .541 .86 160 3830 4190 63 79 175 191 0 6005 344 5661 .617 6248 5904 1.621 .549 -.697 -.866
8 4031 1608 96 305 3935 1303 4402 1617 110 515 4306 1312 0 0 1860 767 76 1712 93 24 92 1 5238 5618 3.02 .331 .305 .379 .305 2.657 156 670 .322 .82 150 4010 4190 63 78 193 208 0 1729 328 1401 .356 1739 1411 2.809 .328 -1.49 -1.61
9 2097 2986 91 280 2006 2706 2412 3322 102 455 2321 3042 0 0 1026 1406 55 1139 89 83 87 73 4712 5363 .741 1.349 1.311 1.429 1.295 1.803 156 674 1.962 .76 150 4210 4190 63 78 213 228 0 3211 301 2910 1.45 3572 3271 .689 1.409 .537 .495
10 206 421 87 293 119 128 200 384 99 435 113 91 0 0 72 238 59 1156 82 0 47 0 247 204 .93 1.076 .805 1.54 1.415 3.097 156 645 56.451 .14 150 4390 4190 63 78 231 246 0 453 315 138 1.157 413 98 .865 .866 .21 -.208
11 321 415 85 284 236 131 329 383 96 406 244 99 0 0 116 203 48 876 91 0 85 0 367 343 1.802 .555 .406 .639 .691 3.323 156 628 7.521 .28 140 4580 4190 64 78 251 265 0 446 305 141 .597 412 106 1.675 .436 -.745 -1.197
12 189 385 89 282 100 103 144 301 96 356 55 19 0 0 121 432 37 413 51 10 47 1 203 74 .971 1.03 .345 1.887 1.885 4.798 156 722 16.589 .26 150 4770 4180 62 77 269 284 0 414 303 111 1.108 324 20 .903 .371 .147 -1.429
13 1054 2941 88 291 966 2650 1199 3073 97 349 1111 2782 0 0 768 2373 39 342 75 74 72 70 3616 3893 .365 2.743 2.504 3.2 2.556 2.252 208 767 3.297 .86 160 4960 4190 63 79 288 304 0 3162 313 2849 2.95 3304 2991 .339 2.693 1.561 1.429
14 263 640 84 280 179 360 270 618 93 325 186 338 0 0 96 251 42 226 89 66 85 35 539 524 .497 2.011 1.817 1.851 1.981 2.416 156 643 4.272 .59 150 5150 4190 63 78 307 322 0 688 301 387 2.163 665 363 .462 1.954 1.113 .966
15 227 471 87 283 140 188 235 442 97 333 148 159 0 0 124 269 43 324 68 26 63 5 328 307 .745 1.343 1.074 1.724 1.641 3.405 208 836 7.456 .39 160 5340 4190 63 79 326 342 0 506 304 202 1.444 475 171 .693 1.155 .53 .208
16 3755 1645 95 278 3660 1367 3819 1638 517 1743 3724 1360 0 0 1745 681 2950 9215 75 0 9 0 5027 5084 2.677 .373 .365 .414 .359 2.068 120 542 3.528 .8 130 5530 4180 63 76 346 359 0 1769 299 1470 .402 1761 1462 2.49 .393 -1.316 -1.349
17 286 1120 90 276 196 844 284 377 379 1284 194 101 0 0 215 5416 2436 7611 0 1 0 1 1040 295 .232 4.306 .521 1.111 1.112 4.231 208 800 4.131 .88 160 5710 4200 64 80 363 379 0 1204 297 908 4.63 405 109 .216 .56 2.211 -.837
18 197 368 84 259 113 109 137 329 93 301 53 70 0 0 149 241 43 245 57 21 39 6 222 123 1.037 .965 1.321 1.85 1.756 3.537 156 638 11.784 .28 140 5910 4180 63 77 384 398 0 396 278 117 1.037 354 75 .964 1.42 .053 .506
19 252 417 84 263 168 154 266 357 95 401 182 94 0 0 140 273 44 1399 72 0 66 0 322 276 1.091 .917 .516 1.071 .98 4.494 208 762 46.665 .23 160 6100 4190 63 79 402 418 0 448 283 166 .986 384 101 1.015 .555 -.021 -.849
20 185 344 84 251 101 93 161 307 94 359 77 56 0 0 107 205 49 1300 62 0 41 0 194 133 1.086 .921 .727 1.435 1.677 3.15 156 558 44.756 .34 140 6290 4190 64 78 422 436 0 370 270 100 .99 330 60 1.01 .782 -.014 -.355

Total number of rows: 7680

Table truncated, full table size 1697 Kbytes.




Supplementary data files not provided
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