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Sample GSM90632 Query DataSets for GSM90632
Status Public on Jan 05, 2006
Title fibroblast 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 fibroblast cell line
Organism Mus musculus
Characteristics fibroblast cell line
Extracted molecule total RNA
Label Cy5
 
 
Description Simple annotation: Primary tissue, mouse
Image: http://smd.stanford.edu/MicroArray/gifs/2001-09/20344.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 1276 2608 164 199 1112 2409 1504 3161 168 207 1340 2962 0 0 776 1634 39 90 80 82 75 76 3521 4302 .462 2.166 2.21 2.246 2.195 1.922 208 1000 2.186 .97 160 2930 4170 53 69 65 81 0 2329 178 2151 1.934 2822 2645 .517 1.974 .952 .981
2 565 513 162 196 403 317 651 451 165 206 489 255 0 0 268 403 40 89 78 70 76 61 720 744 1.271 .787 .521 .759 .664 2.901 208 725 1.279 .57 160 3120 4170 53 69 84 100 0 458 175 283 .702 403 228 1.424 .466 -.51 -1.103
3 554 490 162 196 392 294 586 477 164 206 424 281 0 0 177 222 41 87 91 82 89 71 686 705 1.333 .75 .663 .679 .706 2.166 156 605 .904 .71 150 3310 4170 53 68 103 118 0 438 175 263 .67 426 251 1.493 .592 -.579 -.757
4 925 698 161 187 764 511 975 704 164 202 814 517 0 0 604 426 41 132 76 72 71 65 1275 1331 1.495 .669 .635 .711 .68 2.091 208 727 .67 .9 160 3500 4160 52 68 122 138 0 623 167 456 .597 629 462 1.675 .567 -.744 -.818
5 688 641 162 178 526 463 745 579 182 231 583 401 0 0 342 482 356 767 69 12 34 3 989 984 1.136 .88 .688 .902 .773 2.76 208 679 1.203 .64 160 3690 4170 53 69 141 157 0 572 159 413 .786 517 358 1.272 .614 -.348 -.703
6 524 366 166 186 358 180 619 273 186 236 453 87 0 0 270 351 357 770 60 4 4 1 538 540 1.989 .503 .192 .556 .43 4.095 208 673 2.237 .78 160 3880 4160 52 68 160 176 0 327 166 161 .449 244 78 2.228 .171 -1.155 -2.544
7 2610 5026 167 192 2443 4834 2312 4437 171 207 2145 4245 0 0 2211 4370 41 95 77 85 74 80 7277 6390 .505 1.979 1.979 2.238 1.997 1.942 208 611 1.995 .98 160 4070 4170 53 69 179 195 0 4488 171 4316 1.767 3962 3790 .566 1.767 .821 .821
8 1997 2255 166 207 1831 2048 1974 2147 171 214 1808 1940 0 0 1574 1731 42 96 83 81 78 78 3879 3748 .894 1.119 1.073 1.313 1.157 2.124 208 665 1.114 .97 160 4260 4160 52 68 198 214 0 2013 185 1829 .999 1917 1732 1.001 .958 -.002 -.062
9 839 784 162 197 677 587 912 732 167 211 750 535 0 0 536 516 43 97 77 76 74 72 1264 1285 1.153 .867 .713 .939 .859 2.101 208 706 .916 .91 160 4460 4160 52 68 218 234 0 700 176 524 .774 654 478 1.292 .637 -.369 -.651
10 580 348 162 189 418 159 610 341 164 195 448 152 0 0 178 124 39 87 94 73 92 40 577 600 2.629 .38 .339 .378 .384 2.634 156 609 .391 .58 150 4640 4160 52 67 236 251 0 311 169 142 .34 304 136 2.944 .303 -1.558 -1.723
11 631 653 163 190 468 463 723 722 165 199 560 532 0 0 328 345 38 101 79 77 76 71 931 1092 1.011 .989 .95 .968 1.018 2.28 208 773 1.058 .86 160 4830 4160 52 68 255 271 0 583 170 413 .883 645 475 1.132 .848 -.179 -.237
12 617 549 164 186 453 363 652 512 167 205 488 326 0 0 309 348 42 106 91 70 85 60 816 814 1.248 .801 .668 .778 .783 1.914 120 556 .955 .85 130 5030 4150 52 65 276 289 0 490 166 324 .715 457 291 1.398 .596 -.483 -.746
13 1715 1472 167 190 1548 1282 1800 1359 171 203 1633 1169 0 0 1201 1074 41 88 84 84 80 78 2830 2802 1.207 .828 .716 .875 .825 1.984 208 728 .855 .96 170 5220 4170 52 69 293 310 0 1314 170 1145 .739 1213 1044 1.352 .639 -.436 -.646
14 696 314 170 191 526 123 817 299 171 202 647 108 0 0 376 150 41 90 79 53 75 34 649 755 4.276 .234 .167 .291 .262 3.359 208 645 .212 .5 160 5400 4160 52 68 312 328 0 280 171 110 .209 267 96 4.79 .149 -2.26 -2.746
15 592 382 169 191 423 191 671 355 171 202 502 164 0 0 297 204 43 102 80 65 75 41 614 666 2.215 .452 .327 .536 .481 3.214 208 686 .475 .59 160 5600 4160 52 68 332 348 0 341 171 171 .403 317 146 2.48 .292 -1.311 -1.777
16 1271 983 170 194 1101 789 1250 880 172 206 1080 686 0 0 918 700 43 101 78 79 74 71 1890 1766 1.395 .717 .635 .793 .72 1.992 208 710 .733 .96 160 5780 4160 52 68 350 366 0 878 173 704 .64 786 613 1.563 .567 -.644 -.818
17 504 313 169 196 335 117 565 297 170 205 396 101 0 0 250 144 42 91 77 52 71 37 452 497 2.863 .349 .255 .478 .47 3.46 208 777 .4 .55 160 5980 4160 52 68 370 386 0 279 175 104 .312 265 90 3.207 .228 -1.681 -2.135
18 922 1278 169 198 753 1080 806 1107 172 211 637 909 0 0 641 1015 43 98 92 83 88 77 1833 1546 .697 1.434 1.427 1.193 1.361 2.491 80 390 1.575 .95 110 6160 4170 55 66 390 401 0 1141 177 964 1.281 988 812 .781 1.274 .357 .349
19 636 427 167 195 469 232 696 412 169 213 529 217 0 0 220 167 43 106 92 76 89 51 701 746 2.022 .495 .41 .475 .5 2.353 156 688 .624 .59 150 6350 4160 52 67 407 422 0 381 174 207 .442 368 194 2.264 .366 -1.179 -1.449
20 629 759 165 192 464 567 624 736 167 208 459 544 0 0 291 465 41 104 90 81 86 74 1031 1003 .818 1.222 1.185 1.143 1.225 1.939 156 654 1.455 .87 150 6540 4160 52 67 426 441 0 678 171 506 1.091 657 486 .917 1.058 .126 .082

Total number of rows: 7680

Table truncated, full table size 1746 Kbytes.




Supplementary data files not provided
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